Memory	4
Segmentation File	/cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/cptac3_luad_cnv.v3.TP53.seg.txt
Markers File	./this_file_does_not_exist.txt
Max Marker Spacing	10000
Reference Genome	/cromwell_root/broad-institute-gdac/gdc/reference/gistic/gistic2.refgene.hg38.UCSC.add_miR.160920.mat
CNV Files	/cromwell_root/broad-institute-gdac/gdc/reference/gistic/hg38_GDC_SNP6_CNV_list.161107.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