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]
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	broad_significance_results.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	broad_significance_results.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	hg19_with_miR_20120227.mat	GISTIC	Level_4	matlab	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	CNV.hg19.bypos.111213.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_lesions.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_lesions.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_thresholded.by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_thresholded.by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_qplot.fig	GISTIC	Level_4	fig	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_qplot.fig	GISTIC	Level_4	fig	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	broad_values_by_arm.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	broad_values_by_arm.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_qplot.fig	GISTIC	Level_4	fig	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_qplot.fig	GISTIC	Level_4	fig	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	focal_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	focal_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	focal_input.seg.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	focal_input.seg.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	freqarms_vs_ngenes.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	freqarms_vs_ngenes.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	scores.gistic	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	scores.gistic	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	table_amp.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	table_amp.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	table_del.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	table_del.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	arraylistfile.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	arraylistfile.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	raw_copy_number.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	raw_copy_number.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
markers_file	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_qplot.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_genes.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	broad_significance_results.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	broad_significance_results.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	hg19_with_miR_20120227.mat	GISTIC	Level_4	matlab	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	CNV.hg19.bypos.111213.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
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Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	table_amp.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	table_del.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	table_del.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	arraylistfile.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	arraylistfile.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	raw_copy_number.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	raw_copy_number.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:refgene_file	hg19_with_miR_20120227.mat	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
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Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_lesions.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_lesions.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_thresholded.by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	all_thresholded.by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_qplot.fig	GISTIC	Level_4	fig	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	amp_qplot.fig	GISTIC	Level_4	fig	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	broad_values_by_arm.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	broad_values_by_arm.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_qplot.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_qplot.fig	GISTIC	Level_4	fig	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	del_qplot.fig	GISTIC	Level_4	fig	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	focal_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	focal_data_by_genes.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	focal_input.seg.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	focal_input.seg.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	freqarms_vs_ngenes.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	freqarms_vs_ngenes.pdf	GISTIC	Level_4	pdf	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	scores.gistic	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	scores.gistic	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	table_amp.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	table_amp.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	table_del.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	table_del.conf_99.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	arraylistfile.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	arraylistfile.txt	GISTIC	Level_4	text	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	raw_copy_number.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	raw_copy_number.png	GISTIC	Level_4	png	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
Gistic2_Analysis:cnv_files	CNV.hg19.bypos.111213.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:10528:2	CopyNumber_Gistic2_2013092300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0	yes
