# Created: Sat Feb 25 14:56:48 EST 2012 by cgaadm_deadline
# Job: 56346    server:  http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/
# Module: Gistic2_Analysis urn:lsid:broadinstitute.org:cancer.genome.analysis:00264:102
# Parameters: 
#    seg_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA/781709/1.GDAC_MergeDataFiles.Finished/BRCA.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt
#    markers_file = file:/xchip/tcga/CancerGenomeAnalysisData/trunk/markerfiles/gistic_ovarian/broad.probes.txt
#    refgene_file = file:/xchip/cga/reference/gistic/hg18_with_miR_20091116.mat
#    cnv_files = /xchip/cga/reference/gistic2/pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt,/xchip/cga/reference/gistic2/xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.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
