TCGA uveal melanoma (UVM) somatic mutation (bcm automated)

{"start_index":1,"owner":"TCGA","longTitle":"TCGA uveal melanoma (UVM) somatic mutation (bcgsc automated)","cohort":"TCGA Ocular melanomas (UVM)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/uvm/gsc/bcgsc.ca/illuminahiseq_dnaseq_automated/mutations/","dataSubType":"somatic mutation (SNPs and small INDELs)","security":"public","label":"bcgsc automated","method":"BCGSC pipeline","tags":["cancer"],"path":"data/public/TCGA/UVM/mutation_bcgsc","anatomical_origin":["Eye"],"name":"TCGA.UVM.sampleMap/mutation_bcgsc","dataproducer":"Michael Smith Genome Sciences Centre (British Columbia Genome Sciences Centre, BCGSC)","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":["Michael Smith Genome Sciences Centre (British Columbia Genome Sciences Centre, BCGSC)"],"primary_disease":"uveal melanoma","platform":"IlluminaHiSeq","description":"TCGA uveal melanoma (UVM) 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.","wholegenome":true}

TCGA uveal melanoma (UVM) somatic mutation (bcgsc automated)

{"longTitle":"TCGA uveal melanoma (UVM) gene-level nonsilent somatic mutation (broad automated)","cohort":"TCGA Ocular melanomas (UVM)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/uvm/gsc/broad.mit.edu/illuminaga_dnaseq_automated/mutations/","probeMap":"probeMap/hugo_gencode_good_hg19_V24lift37_probemap","dataSubType":"somatic non-silent mutation (gene-level)","security":"public","label":"broad automated","method":"MuTect","tags":["cancer"],"path":"data/public/TCGA/UVM/mutation_broad_gene","anatomical_origin":["Eye"],"name":"TCGA.UVM.sampleMap/mutation_broad_gene","dataproducer":"Broad Institute Genome Sequencing Center","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":["Broad Institute Genome Sequencing Center"],"unit":"binary non-silent mutation","primary_disease":"uveal melanoma","platform":"IlluminaGA","description":"TCGA uveal melanoma (UVM) 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. <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>"}