Complete rewrite of GATK Somatic Variant Pipeline
Complete rewrite of GATK Somatic Variant Pipeline

Tested end-to-end run with no failures. 350 minutes (~6 hours) on a
pair of 5 Gigabyte Tumor/Normal bams.

fnothaft/toil-scripts,jpfeil/toil-scripts,BD2KGenomics/toil-scripts,fnothaft/toil-scripts,jpfeil/toil-scripts,BD2KGenomics/toil-scripts