Memory	4
Segmentation File	/cromwell_root/fc-secure-281e11fc-8f18-46e9-9557-02df8b786c7e/12ca3832-38b1-4687-a2bb-d3effba8e701/aggregate_data_workflow/2476f6f0-ed7c-4e9b-9547-7e89dd5a49e6/call-aggregate_data/LSCC-WXS-TP_NB.CNV__wxs.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