OUTPUT_DIR=/home/goo/gotcloudTutorial UMAKE_ROOT=/usr/local/gotcloud .DELETE_ON_ERROR: all: all20 all20: split20 filt20 pvcf20 vcf20 glf20 split20: $(OUTPUT_DIR)/split/chr20/chr20.filtered.PASS.split.vcflist $(OUTPUT_DIR)/split/chr20/subset.OK: filt20 mkdir --p $(OUTPUT_DIR)/split/chr20 (zcat $(OUTPUT_DIR)/vcfs/chr20/chr20.filtered.vcf.gz | head -100 | grep ^#; zcat $(OUTPUT_DIR)/vcfs/chr20/chr20.filtered.vcf.gz | grep -w PASS;) | $(UMAKE_ROOT)/bin/bgzip -c > $(OUTPUT_DIR)/split/chr20/chr20.filtered.PASS.vcf.gz touch $(OUTPUT_DIR)/split/chr20/subset.OK $(OUTPUT_DIR)/split/chr20/chr20.filtered.PASS.split.vcflist: $(OUTPUT_DIR)/split/chr20/subset.OK mkdir --p $(OUTPUT_DIR)/split/chr20 perl $(UMAKE_ROOT)/scripts/vcfSplit.pl --in $(OUTPUT_DIR)/split/chr20/chr20.filtered.PASS.vcf.gz --out $(OUTPUT_DIR)/split/chr20/chr20.filtered.PASS.split --nunit 10000 --noverlap 1000 2> $(OUTPUT_DIR)/split/chr20/chr20.filtered.PASS.split.err pvcf20: $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00096.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00100.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00103.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00106.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00108.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00111.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00112.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00114.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00115.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00116.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00117.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00118.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00119.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00120.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00122.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00123.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00124.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00125.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00126.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00127.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00131.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00133.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00136.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00137.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00138.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00139.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00140.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00141.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00142.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00143.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00145.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00146.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00148.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00149.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00150.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00151.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00152.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00154.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00155.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00156.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00157.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00158.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00159.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00160.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00231.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00232.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00233.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00239.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00242.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00243.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00244.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00245.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00246.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00247.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00249.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00250.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00251.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00252.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00253.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00254.bam.20.40000001.45000000.vcf.gz.OK vcf20 $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.vcf.OK cut -f 1-8 $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.vcf > $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf touch $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00096.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00096.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00096.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00096.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00096.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00096.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00100.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00100.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00100.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00100.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00100.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00100.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00103.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00103.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00103.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00103.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00103.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00103.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00106.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00106.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00106.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00106.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00106.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00106.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00108.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00108.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00108.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00108.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00108.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00108.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00111.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00111.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00111.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00111.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00111.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00111.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00112.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00112.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00112.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00112.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00112.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00112.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00114.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00114.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00114.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00114.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00114.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00114.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00115.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00115.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00115.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00115.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00115.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00115.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00116.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00116.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00116.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00116.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00116.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00116.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00117.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00117.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00117.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00117.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00117.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00117.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00118.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00118.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00118.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00118.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00118.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00118.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00119.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00119.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00119.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00119.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00119.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00119.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00120.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00120.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00120.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00120.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00120.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00120.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00122.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00122.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00122.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00122.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00122.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00122.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00123.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00123.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00123.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00123.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00123.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00123.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00124.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00124.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00124.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00124.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00124.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00124.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00125.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00125.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00125.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00125.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00125.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00125.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00126.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00126.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00126.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00126.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00126.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00126.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00127.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00127.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00127.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00127.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00127.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00127.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00131.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00131.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00131.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00131.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00131.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00131.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00133.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00133.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00133.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00133.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00133.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00133.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00136.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00136.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00136.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00136.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00136.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00136.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00137.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00137.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00137.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00137.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00137.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00137.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00138.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00138.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00138.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00138.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00138.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00138.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00139.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00139.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00139.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00139.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00139.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00139.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00140.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00140.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00140.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00140.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00140.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00140.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00141.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00141.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00141.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00141.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00141.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00141.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00142.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00142.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00142.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00142.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00142.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00142.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00143.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00143.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00143.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00143.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00143.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00143.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00145.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00145.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00145.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00145.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00145.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00145.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00146.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00146.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00146.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00146.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00146.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00146.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00148.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00148.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00148.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00148.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00148.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00148.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00149.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00149.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00149.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00149.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00149.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00149.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00150.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00150.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00150.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00150.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00150.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00150.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00151.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00151.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00151.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00151.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00151.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00151.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00152.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00152.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00152.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00152.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00152.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00152.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00154.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00154.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00154.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00154.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00154.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00154.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00155.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00155.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00155.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00155.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00155.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00155.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00156.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00156.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00156.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00156.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00156.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00156.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00157.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00157.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00157.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00157.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00157.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00157.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00158.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00158.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00158.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00158.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00158.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00158.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00159.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00159.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00159.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00159.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00159.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00159.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00160.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00160.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00160.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00160.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00160.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00160.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00231.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00231.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00231.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00231.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00231.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00231.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00232.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00232.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00232.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00232.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00232.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00232.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00233.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00233.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00233.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00233.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00233.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00233.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00239.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00239.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00239.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00239.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00239.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00239.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00242.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00242.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00242.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00242.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00242.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00242.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00243.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00243.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00243.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00243.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00243.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00243.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00244.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00244.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00244.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00244.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00244.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00244.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00245.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00245.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00245.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00245.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00245.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00245.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00246.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00246.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00246.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00246.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00246.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00246.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00247.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00247.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00247.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00247.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00247.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00247.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00249.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00249.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00249.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00249.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00249.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00249.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00250.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00250.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00250.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00250.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00250.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00250.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00251.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00251.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00251.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00251.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00251.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00251.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00252.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00252.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00252.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00252.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00252.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00252.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00253.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00253.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00253.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00253.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00253.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00253.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00254.bam.20.40000001.45000000.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf.OK mkdir --p $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/vcfPileup -i $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.sites.vcf -v $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00254.bam.20.40000001.45000000.vcf.gz -b /opt/gotcloudExample/bams/HG00254.bam > $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00254.bam.20.40000001.45000000.vcf.gz.log 2> $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00254.bam.20.40000001.45000000.vcf.gz.err touch $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00254.bam.20.40000001.45000000.vcf.gz.OK filt20: $(OUTPUT_DIR)/vcfs/chr20/chr20.filtered.vcf.gz.OK $(OUTPUT_DIR)/vcfs/chr20/chr20.filtered.vcf.gz.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.stats.vcf.OK $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.vcf.OK $(OUTPUT_DIR)/vcfs/chr20/chr20.merged.vcf.OK perl $(UMAKE_ROOT)/scripts/bams2vcfMerge.pl 5000000 $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.stats.vcf > $(OUTPUT_DIR)/vcfs/chr20/chr20.merged.stats.vcf $(UMAKE_ROOT)/bin/vcfCooker --write-vcf --filter --maxDP 1200 --minDP 60 --maxABL 70 --maxAOI 5 --maxSTR 20 --maxSTZ 5 --minFIC -20 --minSTR -20 --minSTZ -5 --winIndel 5 --indelVCF /opt/gotcloudExample/chr20Ref/1kg.pilot_release.merged.indels.sites.hg19.chr20.vcf --out $(OUTPUT_DIR)/vcfs/chr20/chr20.filtered.sites.vcf --in-vcf $(OUTPUT_DIR)/vcfs/chr20/chr20.merged.stats.vcf perl $(UMAKE_ROOT)/scripts/vcfPaste.pl $(OUTPUT_DIR)/vcfs/chr20/chr20.filtered.sites.vcf $(OUTPUT_DIR)/vcfs/chr20/chr20.merged.vcf | $(UMAKE_ROOT)/bin/bgzip -c > $(OUTPUT_DIR)/vcfs/chr20/chr20.filtered.vcf.gz $(UMAKE_ROOT)/bin/tabix -f -pvcf $(OUTPUT_DIR)/vcfs/chr20/chr20.filtered.vcf.gz perl $(UMAKE_ROOT)/scripts/vcf-summary --vcf $(OUTPUT_DIR)/vcfs/chr20/chr20.filtered.sites.vcf --ref /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa --dbsnp /opt/gotcloudExample/chr20Ref/dbsnp135_chr20.vcf.gz --FNRvcf /opt/gotcloudExample/chr20Ref/hapmap_3.3.b37.sites.chr20.vcf.gz --chr 20 --tabix $(UMAKE_ROOT)/bin/tabix > $(OUTPUT_DIR)/vcfs/chr20/chr20.filtered.sites.vcf.summary touch $(OUTPUT_DIR)/vcfs/chr20/chr20.filtered.vcf.gz.OK $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.stats.vcf.OK: $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00096.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00100.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00103.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00106.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00108.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00111.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00112.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00114.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00115.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00116.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00117.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00118.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00119.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00120.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00122.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00123.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00124.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00125.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00126.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00127.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00131.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00133.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00136.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00137.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00138.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00139.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00140.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00141.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00142.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00143.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00145.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00146.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00148.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00149.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00150.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00151.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00152.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00154.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00155.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00156.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00157.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00158.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00159.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00160.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00231.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00232.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00233.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00239.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00242.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00243.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00244.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00245.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00246.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00247.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00249.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00250.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00251.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00252.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00253.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/HG00254.bam.20.40000001.45000000.vcf.gz.OK $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.vcf.OK $(UMAKE_ROOT)/bin/infoCollector --anchor $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.vcf --prefix $(OUTPUT_DIR)/pvcfs/chr20/40000001.45000000/ --suffix .20.40000001.45000000.vcf.gz --outvcf $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.stats.vcf --index /opt/gotcloudExample/GBR60bam.index 2> $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.stats.vcf.err touch $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.stats.vcf.OK vcf20: $(OUTPUT_DIR)/vcfs/chr20/chr20.merged.vcf.OK $(OUTPUT_DIR)/vcfs/chr20/chr20.merged.vcf.OK: $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.vcf.OK perl $(UMAKE_ROOT)/scripts/bams2vcfMerge.pl 5000000 $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.vcf > $(OUTPUT_DIR)/vcfs/chr20/chr20.merged.vcf cut -f 1-8 $(OUTPUT_DIR)/vcfs/chr20/chr20.merged.vcf > $(OUTPUT_DIR)/vcfs/chr20/chr20.merged.sites.vcf touch $(OUTPUT_DIR)/vcfs/chr20/chr20.merged.vcf.OK $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.vcf.OK: $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00096.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00100.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00103.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00106.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00108.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00111.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00112.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00114.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00115.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00116.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00117.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00118.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00119.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00120.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00122.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00123.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00124.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00125.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00126.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00127.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00131.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00133.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00136.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00137.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00138.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00139.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00140.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00141.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00142.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00143.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00145.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00146.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00148.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00149.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00150.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00151.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00152.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00154.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00155.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00156.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00157.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00158.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00159.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00160.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00231.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00232.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00233.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00239.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00242.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00243.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00244.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00245.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00246.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00247.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00249.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00250.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00251.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00252.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00253.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00254.20.40000001.45000000.glf.OK mkdir --p $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/glfMultiples --minMapQuality 0 --minDepth 1 --maxDepth 10000000 --uniformTsTv --smartFilter --ped $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/glfIndex.ped -b $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.vcf > $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.vcf.log 2> $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.vcf.err touch $(OUTPUT_DIR)/vcfs/chr20/40000001.45000000/chr20.40000001.45000000.vcf.OK glf20: $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00096.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00100.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00103.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00106.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00108.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00111.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00112.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00114.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00115.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00116.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00117.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00118.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00119.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00120.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00122.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00123.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00124.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00125.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00126.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00127.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00131.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00133.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00136.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00137.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00138.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00139.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00140.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00141.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00142.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00143.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00145.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00146.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00148.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00149.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00150.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00151.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00152.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00154.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00155.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00156.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00157.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00158.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00159.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00160.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00231.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00232.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00233.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00239.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00242.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00243.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00244.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00245.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00246.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00247.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00249.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00250.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00251.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00252.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00253.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00254.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00096.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00096.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00096.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00096.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00100.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00100.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00100.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00100.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00103.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00103.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00103.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00103.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00106.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00106.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00106.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00106.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00108.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00108.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00108.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00108.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00111.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00111.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00111.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00111.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00112.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00112.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00112.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00112.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00114.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00114.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00114.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00114.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00115.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00115.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00115.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00115.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00116.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00116.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00116.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00116.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00117.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00117.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00117.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00117.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00118.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00118.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00118.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00118.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00119.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00119.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00119.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00119.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00120.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00120.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00120.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00120.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00122.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00122.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00122.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00122.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00123.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00123.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00123.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00123.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00124.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00124.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00124.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00124.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00125.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00125.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00125.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00125.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00126.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00126.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00126.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00126.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00127.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00127.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00127.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00127.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00131.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00131.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00131.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00131.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00133.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00133.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00133.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00133.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00136.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00136.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00136.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00136.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00137.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00137.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00137.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00137.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00138.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00138.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00138.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00138.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00139.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00139.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00139.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00139.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00140.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00140.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00140.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00140.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00141.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00141.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00141.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00141.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00142.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00142.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00142.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00142.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00143.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00143.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00143.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00143.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00145.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00145.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00145.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00145.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00146.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00146.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00146.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00146.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00148.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00148.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00148.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00148.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00149.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00149.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00149.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00149.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00150.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00150.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00150.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00150.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00151.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00151.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00151.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00151.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00152.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00152.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00152.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00152.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00154.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00154.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00154.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00154.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00155.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00155.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00155.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00155.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00156.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00156.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00156.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00156.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00157.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00157.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00157.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00157.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00158.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00158.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00158.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00158.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00159.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00159.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00159.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00159.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00160.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00160.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00160.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00160.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00231.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00231.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00231.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00231.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00232.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00232.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00232.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00232.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00233.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00233.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00233.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00233.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00239.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00239.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00239.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00239.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00242.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00242.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00242.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00242.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00243.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00243.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00243.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00243.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00244.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00244.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00244.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00244.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00245.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00245.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00245.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00245.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00246.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00246.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00246.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00246.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00247.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00247.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00247.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00247.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00249.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00249.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00249.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00249.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00250.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00250.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00250.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00250.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00251.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00251.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00251.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00251.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00252.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00252.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00252.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00252.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00253.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00253.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00253.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00253.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00254.20.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00254.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00254.20.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/samples/chr20/40000001.45000000/HG00254.20.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00096/chr20/HG00096.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00096/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00096.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00096/chr20/HG00096.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00096/chr20/HG00096.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00100/chr20/HG00100.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00100/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00100.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00100/chr20/HG00100.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00100/chr20/HG00100.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00103/chr20/HG00103.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00103/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00103.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00103/chr20/HG00103.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00103/chr20/HG00103.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00106/chr20/HG00106.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00106/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00106.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00106/chr20/HG00106.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00106/chr20/HG00106.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00108/chr20/HG00108.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00108/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00108.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00108/chr20/HG00108.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00108/chr20/HG00108.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00111/chr20/HG00111.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00111/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00111.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00111/chr20/HG00111.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00111/chr20/HG00111.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00112/chr20/HG00112.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00112/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00112.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00112/chr20/HG00112.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00112/chr20/HG00112.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00114/chr20/HG00114.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00114/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00114.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00114/chr20/HG00114.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00114/chr20/HG00114.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00115/chr20/HG00115.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00115/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00115.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00115/chr20/HG00115.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00115/chr20/HG00115.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00116/chr20/HG00116.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00116/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00116.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00116/chr20/HG00116.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00116/chr20/HG00116.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00117/chr20/HG00117.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00117/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00117.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00117/chr20/HG00117.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00117/chr20/HG00117.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00118/chr20/HG00118.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00118/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00118.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00118/chr20/HG00118.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00118/chr20/HG00118.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00119/chr20/HG00119.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00119/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00119.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00119/chr20/HG00119.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00119/chr20/HG00119.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00120/chr20/HG00120.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00120/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00120.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00120/chr20/HG00120.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00120/chr20/HG00120.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00122/chr20/HG00122.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00122/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00122.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00122/chr20/HG00122.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00122/chr20/HG00122.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00123/chr20/HG00123.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00123/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00123.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00123/chr20/HG00123.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00123/chr20/HG00123.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00124/chr20/HG00124.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00124/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00124.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00124/chr20/HG00124.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00124/chr20/HG00124.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00125/chr20/HG00125.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00125/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00125.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00125/chr20/HG00125.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00125/chr20/HG00125.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00126/chr20/HG00126.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00126/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00126.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00126/chr20/HG00126.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00126/chr20/HG00126.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00127/chr20/HG00127.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00127/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00127.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00127/chr20/HG00127.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00127/chr20/HG00127.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00131/chr20/HG00131.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00131/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00131.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00131/chr20/HG00131.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00131/chr20/HG00131.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00133/chr20/HG00133.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00133/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00133.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00133/chr20/HG00133.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00133/chr20/HG00133.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00136/chr20/HG00136.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00136/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00136.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00136/chr20/HG00136.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00136/chr20/HG00136.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00137/chr20/HG00137.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00137/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00137.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00137/chr20/HG00137.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00137/chr20/HG00137.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00138/chr20/HG00138.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00138/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00138.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00138/chr20/HG00138.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00138/chr20/HG00138.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00139/chr20/HG00139.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00139/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00139.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00139/chr20/HG00139.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00139/chr20/HG00139.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00140/chr20/HG00140.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00140/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00140.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00140/chr20/HG00140.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00140/chr20/HG00140.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00141/chr20/HG00141.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00141/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00141.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00141/chr20/HG00141.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00141/chr20/HG00141.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00142/chr20/HG00142.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00142/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00142.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00142/chr20/HG00142.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00142/chr20/HG00142.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00143/chr20/HG00143.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00143/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00143.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00143/chr20/HG00143.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00143/chr20/HG00143.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00145/chr20/HG00145.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00145/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00145.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00145/chr20/HG00145.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00145/chr20/HG00145.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00146/chr20/HG00146.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00146/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00146.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00146/chr20/HG00146.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00146/chr20/HG00146.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00148/chr20/HG00148.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00148/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00148.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00148/chr20/HG00148.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00148/chr20/HG00148.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00149/chr20/HG00149.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00149/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00149.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00149/chr20/HG00149.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00149/chr20/HG00149.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00150/chr20/HG00150.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00150/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00150.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00150/chr20/HG00150.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00150/chr20/HG00150.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00151/chr20/HG00151.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00151/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00151.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00151/chr20/HG00151.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00151/chr20/HG00151.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00152/chr20/HG00152.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00152/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00152.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00152/chr20/HG00152.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00152/chr20/HG00152.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00154/chr20/HG00154.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00154/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00154.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00154/chr20/HG00154.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00154/chr20/HG00154.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00155/chr20/HG00155.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00155/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00155.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00155/chr20/HG00155.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00155/chr20/HG00155.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00156/chr20/HG00156.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00156/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00156.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00156/chr20/HG00156.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00156/chr20/HG00156.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00157/chr20/HG00157.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00157/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00157.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00157/chr20/HG00157.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00157/chr20/HG00157.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00158/chr20/HG00158.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00158/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00158.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00158/chr20/HG00158.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00158/chr20/HG00158.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00159/chr20/HG00159.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00159/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00159.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00159/chr20/HG00159.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00159/chr20/HG00159.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00160/chr20/HG00160.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00160/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00160.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00160/chr20/HG00160.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00160/chr20/HG00160.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00231/chr20/HG00231.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00231/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00231.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00231/chr20/HG00231.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00231/chr20/HG00231.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00232/chr20/HG00232.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00232/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00232.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00232/chr20/HG00232.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00232/chr20/HG00232.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00233/chr20/HG00233.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00233/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00233.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00233/chr20/HG00233.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00233/chr20/HG00233.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00239/chr20/HG00239.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00239/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00239.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00239/chr20/HG00239.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00239/chr20/HG00239.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00242/chr20/HG00242.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00242/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00242.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00242/chr20/HG00242.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00242/chr20/HG00242.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00243/chr20/HG00243.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00243/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00243.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00243/chr20/HG00243.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00243/chr20/HG00243.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00244/chr20/HG00244.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00244/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00244.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00244/chr20/HG00244.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00244/chr20/HG00244.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00245/chr20/HG00245.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00245/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00245.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00245/chr20/HG00245.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00245/chr20/HG00245.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00246/chr20/HG00246.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00246/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00246.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00246/chr20/HG00246.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00246/chr20/HG00246.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00247/chr20/HG00247.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00247/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00247.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00247/chr20/HG00247.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00247/chr20/HG00247.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00249/chr20/HG00249.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00249/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00249.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00249/chr20/HG00249.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00249/chr20/HG00249.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00250/chr20/HG00250.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00250/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00250.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00250/chr20/HG00250.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00250/chr20/HG00250.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00251/chr20/HG00251.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00251/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00251.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00251/chr20/HG00251.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00251/chr20/HG00251.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00252/chr20/HG00252.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00252/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00252.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00252/chr20/HG00252.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00252/chr20/HG00252.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00253/chr20/HG00253.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00253/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00253.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00253/chr20/HG00253.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00253/chr20/HG00253.bam.40000001.45000000.glf.OK $(OUTPUT_DIR)/glfs/bams/HG00254/chr20/HG00254.bam.40000001.45000000.glf.OK: mkdir --p $(OUTPUT_DIR)/glfs/bams/HG00254/chr20 $(UMAKE_ROOT)/bin/samtools-hybrid view -q 20 -F 0x0704 -uh /opt/gotcloudExample/bams/HG00254.bam 20:40000001-45000000 | $(UMAKE_ROOT)/bin/samtools-hybrid calmd -AEbr - /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa 2> /dev/null | $(UMAKE_ROOT)/bin/bam clipOverlap --in -.bam --out -.ubam | $(UMAKE_ROOT)/bin/samtools-hybrid pileup -f /opt/gotcloudExample/chr20Ref/human_g1k_v37_chr20.fa -g - > $(OUTPUT_DIR)/glfs/bams/HG00254/chr20/HG00254.bam.40000001.45000000.glf touch $(OUTPUT_DIR)/glfs/bams/HG00254/chr20/HG00254.bam.40000001.45000000.glf.OK