Memory	4
Segmentation File	/cromwell_root/fc-secure-823808d0-5404-49c9-990f-b3d9e353e468/7cb711fc-2bbf-4c6b-ad57-cd8836a24fa7/allelic_capseg_combine_seg/959b0092-a8d3-4eb2-8216-f63d88932383/call-allelic_capseg_combine_seg_task_1/BRCA-freeze-v5.allelic_capseg.seg.txt
Markers File	./this_file_does_not_exist.txt
Max Marker Spacing	10000
Reference Genome	/cromwell_root/broad-institute-gdac/gdc/reference/gistic/hg19_GENCODE_v18_20140127.mat
CNV Files	/cromwell_root/broad-institute-gdac/gdc/reference/gistic/SNP6.merged.151117.hg19.CNV.txt
Amplification Threshold	0.1
Deletion Threshold	0.1
Q-value Threshold	0.25
Cap Values	1.5
Broad Length Cutoff	0.98
Remove X-Chromosome	0
Confidence Level	0.99
Join Segment Size	4
Arm Level Peel Off	1
Maximum Sample Segments	2000
Do Gene GISTIC	1
Gene Collapse Method	extreme