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]
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	table.1.txt	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	txt	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D48V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D8V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D45V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D47V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D8V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D49V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D45V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D43V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D9V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D48V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D47V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D9V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D46V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D46V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D10V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2012122100.0.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	table.1.txt	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	txt	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D48V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D8V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D45V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D47V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D8V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D49V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D45V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D43V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D9V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D48V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D47V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D9V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D46V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D46V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	D10V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	GBM-TP.clin.merged.picked.txt	gdac.broadinstitute.org_GBM-TP.Clinical_Pick_Tier1.Level_4.2012122100.1.0	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:12	Correlate_Clinical_vs_CopyNumber_Focal_2012122100	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_GBM-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2012122100.0.0	yes
