Input parameters: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/Snowman/broadinstitute.org/cancer.genome.analysis/10982/134/ /broad/broadsv/HCC1143/250PE/HCC1143_250PE.mem.bam HCC1143_250_mem 0 -n /broad/broadsv/HCC1143/250PE/HCC1143_BL_250PE.mem.bam -p 4 -D/xchip/gistic/Jeremiah/Projects/SnowmanFilters/dbsnp_138.b37_indel.vcf
time /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/Snowman/broadinstitute.org/cancer.genome.analysis/10982/134//snowman_170106 run -t /broad/broadsv/HCC1143/250PE/HCC1143_250PE.mem.bam -a HCC1143_250_mem -n /broad/broadsv/HCC1143/250PE/HCC1143_BL_250PE.mem.bam -p 4 -D/xchip/gistic/Jeremiah/Projects/SnowmanFilters/dbsnp_138.b37_indel.vcf
...sorting and indexing with 6G memory