This is an old revision of the document!
For sequences from UMICH sequencing core. Example Makefile for converting fastq's for 1 sample to a single recalibrated deduped bam file:
/net/twins/svrieze/vrieze-pipeline/demux/Pool_18158/intermediateFiles/S001/Makefile
For sequences from HudsonAlpha core. Example Makefile for converting bam to fastq back to bam. /net/twins/svrieze/BRIDGES-samples-bams/bwa-mem-conversion/1497-RMM-1540.makefile