Input parameters: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/Snowman/broadinstitute.org/cancer.genome.analysis/10982/134/ /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam 160413_10x_sim 0 -n /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.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 /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam -a 160413_10x_sim -n /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam -p 4 -D/xchip/gistic/Jeremiah/Projects/SnowmanFilters/dbsnp_138.b37_indel.vcf
...sorting and indexing with 6G memory