# Created: Thu Jul 12 16:05:32 EDT 2012 by cgaadm
# Job: 126071    server:  http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/
# Module: Gistic2_Analysis urn:lsid:broadinstitute.org:cancer.genome.analysis:00264:104
# Parameters: 
#    seg_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LIHC/1444794/2.GDAC_MergeDataFiles.Finished/LIHC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
#    markers_file = file:/xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt
#    refgene_file = file:/xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat
#    cnv_files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt
#    amp_thresh = 0.30
#    del_thresh = 0.30
#    cap = 2.0
#    broad.length.cutoff = 0.5
#    remove.X = 1
#    confidence.level = 0.99
#    join.segment.size = 10
#    arm.peel = 1
#    max.sample.segs = 10000
