TCGA thymoma (THYM) copy number gistic2 estimate

{"start_index":1,"owner":"TCGA","longTitle":"TCGA thymoma (THYM) somatic mutation (broad automated)","cohort":"TCGA Thymoma (THYM)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thym/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/","dataSubType":"somatic mutation (SNPs and small INDELs)","security":"public","label":"broad automated","method":"MuTect","tags":["cancer"],"path":"data/public/TCGA/THYM/mutation_broad","anatomical_origin":["Thymus"],"name":"TCGA.THYM.sampleMap/mutation_broad","dataproducer":"Broad Institute Genome Sequencing Center","wrangling_procedure":"Download .maf file from TCGA DCC, removed any calls from WGS samples, processed into UCSC Xena mutation format, stored in the UCSC Xena repository","sample_type":["tumor"],"assembly":"hg19","redistribution":true,"domain":"TCGA","type":"mutationVector","wrangler":"TCGAscript maf processed on 2017-09-08","version":"2017-09-08","gdata_tags":["Broad Institute Genome Sequencing Center"],"primary_disease":"thymoma","platform":"IlluminaGA","description":"TCGA thymoma (THYM) somatic mutation data. Sequencing data are generated on a IlluminaGA system. The calls are generated at Broad Institute Genome Sequencing Center using the MuTect method. When variant allele frequency information is available, only calls with VAF >4.0% are kept, resulting in 0 calls are kept and 0 calls are removed.","wholegenome":true}

TCGA thymoma (THYM) somatic mutation (broad automated)

{"start_index":1,"owner":"TCGA","longTitle":"TCGA thymoma (THYM) somatic mutation (wustl_hiseq automated)","cohort":"TCGA Thymoma (THYM)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thym/gsc/genome.wustl.edu/illuminahiseq_dnaseq_automated/mutations/","dataSubType":"somatic mutation (SNPs and small INDELs)","security":"public","label":"wustl_hiseq automated","method":"WashU pipeline","tags":["cancer"],"path":"data/public/TCGA/THYM/mutation_wustl_hiseq","anatomical_origin":["Thymus"],"name":"TCGA.THYM.sampleMap/mutation_wustl_hiseq","dataproducer":"Genome Institute at Washington University Sequencing Center","wrangling_procedure":"Download .maf file from TCGA DCC, removed any calls from WGS samples, processed into UCSC Xena mutation format, stored in the UCSC Xena repository","sample_type":["tumor"],"assembly":"hg19","redistribution":true,"domain":"TCGA","type":"mutationVector","wrangler":"TCGAscript maf processed on 2017-10-17","version":"2017-10-17","target":"whole exome","gdata_tags":["Genome Institute at Washington University Sequencing Center"],"primary_disease":"thymoma","platform":"IlluminaHiSeq","description":"TCGA thymoma (THYM) somatic mutation data. Sequencing data are generated on a IlluminaHiSeq system. The calls are generated at Genome Institute at Washington University Sequencing Center using the WashU pipeline method."}