These scripts were written by Tom Kono and used for read mapping for Wild Barley Diversity Collection samples.
The WBDC_103_2013-11-20.job script takes fastq.gz files and outputs .sam files.
Process_SAM.job takes .sam files and outputs Finished.bam files.
GATK_RTC.job takes .bam files and outputs Realigned.bam files.
GATK_HaplotypeCaller.job takes .bam files and creates RawVCF_Long_Calhoun.vcf files.
Merge_BAMs.job merges all the .bam files.