TCGA stomach adenocarcinoma (STAD) gene-level nonsilent somatic mutation (ucsc automated)

{"start_index":1,"owner":"TCGA","longTitle":"TCGA stomach adenocarcinoma (STAD) somatic mutation (broad curated)","cohort":"TCGA Stomach Cancer (STAD)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/stad/gsc/broad.mit.edu/illuminaga_dnaseq_curated/mutations/","dataSubType":"somatic mutation (SNPs and small INDELs)","security":"public","label":"broad curated","method":"MuTect","tags":["cancer","gastric cancer"],"path":"data/public/TCGA/STAD/mutation_curated_broad","anatomical_origin":["Stomach"],"name":"TCGA.STAD.sampleMap/mutation_curated_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":"stomach adenocarcinoma","platform":"IlluminaGA","description":"TCGA stomach adenocarcinoma (STAD) 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.","wholegenome":true}

TCGA stomach adenocarcinoma (STAD) somatic mutation (broad curated)

{"longTitle":"TCGA testicular germ cell tumor (TGCT) gene-level nonsilent somatic mutation (bcgsc automated)","cohort":"TCGA Testicular Cancer (TGCT)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/tgct/gsc/bcgsc.ca/illuminahiseq_dnaseq_automated/mutations/","probeMap":"probeMap/hugo_gencode_good_hg19_V24lift37_probemap","dataSubType":"somatic non-silent mutation (gene-level)","security":"public","label":"bcgsc automated","method":"BCGSC pipeline","tags":["cancer"],"path":"data/public/TCGA/TGCT/mutation_bcgsc_gene","anatomical_origin":["Testis"],"name":"TCGA.TGCT.sampleMap/mutation_bcgsc_gene","dataproducer":"Michael Smith Genome Sciences Centre (British Columbia Genome Sciences Centre, BCGSC)","wrangling_procedure":"Download .maf file from TCGA DCC, processed into gene by sample matrix at UCSC, stored in the UCSC Xena repository","sample_type":["tumor"],"redistribution":true,"type":"genomicMatrix","wrangler":"xena TCGAscript maf processed on 2018-01-12","version":"2018-01-12","gdata_tags":["Michael Smith Genome Sciences Centre (British Columbia Genome Sciences Centre, BCGSC)"],"unit":"binary non-silent mutation","primary_disease":"testicular germ cell tumor","platform":"IlluminaHiSeq","description":"TCGA testicular germ cell tumor (TGCT) somatic mutation data.  Sequencing data are generated on a IlluminaHiSeq system. The calls are generated at Michael Smith Genome Sciences Centre (British Columbia Genome Sciences Centre, BCGSC) using the BCGSC pipeline method. <br><br> Red (=1) indicates that a non-silent somatic mutation (nonsense, missense, frame-shif indels, splice site mutations, stop codon readthroughs, change of start codon, inframe indels) was identified in the protein coding region of a gene, or any mutation identified in a non-coding gene. White (=0) indicates that none of the above mutation calls were made in this gene for the specific sample.<br><br>"}