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 first set of 300ish 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

For second set of 180ish 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