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	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	table.1.txt	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	txt	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D3V11.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D26V11.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D2V11.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D11V13.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D7V11.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D3V13.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D11V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D26V13.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D8V13.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D5V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D19V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D1V11.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D12V6.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
cnv2cluster1.sample.gene.table.file	all_lesions.conf_99.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	table.1.txt	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	txt	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D3V11.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D26V11.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D2V11.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D11V13.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D7V11.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D3V13.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D11V2.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D26V13.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D8V13.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D5V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D19V1.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D1V11.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	D12V6.png	Correlation-Clinical_Genes_SignificantlyMutated	Level_4	png	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	nozzle.html	report	Level_4	html	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
Correlate_Clinical_Cnvs_onlysig2.clinical.info.file	THCA-TP.clin.merged.picked.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00496:19	Correlate_Clinical_vs_CopyNumber_Focal_2013052300	nozzle.RData	report	Level_4	RData	gdac.broadinstitute.org_THCA-TP.Correlate_Clinical_vs_CopyNumber_Focal.Level_4.2013052300.0.0	yes
