Pipeline Input Name	Archive Result File REF	Comment [TCGA Archive Name]	Protocol REF	Data Transformation Name	Derived Data File	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Comment [TCGA File Type]	Comment [TCGA Archive Name]	Comment [TCGA Include for Analysis]
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	hg18_with_miR_20091116.mat	GISTIC	Level_4	matlab	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	broad.probes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	amp_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	del_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	table_amp.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	table_del.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	all_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	all_lesions.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	all_thresholded.by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	amp_qplot.v2.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	amp_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	amp_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	broad_significance_results.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	broad_values_by_arm.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	del_qplot.v2.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	del_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	del_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	focal_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	focal_input.seg.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	freqarms_vs_ngenes.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	scores.gistic	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	raw_copy_number.png	GISTIC	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	arraylistfile.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.seg_file	OV.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt	gdac.broadinstitute.org_OV.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.Level_3.2012042500.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	hg18_with_miR_20091116.mat	GISTIC	Level_4	matlab	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	broad.probes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	amp_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	del_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	table_amp.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	table_del.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	all_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	all_lesions.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	all_thresholded.by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	amp_qplot.v2.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	amp_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	amp_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	broad_significance_results.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	broad_values_by_arm.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	del_qplot.v2.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	del_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	del_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	focal_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	focal_input.seg.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	freqarms_vs_ngenes.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	scores.gistic	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	raw_copy_number.png	GISTIC	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	arraylistfile.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.markers_file	broad.probes.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
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Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	broad.probes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	amp_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	del_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
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Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	table_del.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	all_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	all_lesions.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	all_thresholded.by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	amp_qplot.v2.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	amp_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	amp_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	broad_significance_results.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	broad_values_by_arm.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	del_qplot.v2.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	del_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	del_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	focal_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	focal_input.seg.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	freqarms_vs_ngenes.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	scores.gistic	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	raw_copy_number.png	GISTIC	Level_4	png	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	arraylistfile.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
Gistic2_Analysis1.refgene_file	hg18_with_miR_20091116.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00293:94	CopyNumber_Gistic2_2012042500	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_OV.CopyNumber_Gistic2.Level_4.2012042500.0.0	yes
