{"cohort":"PCAWG (donor centric)","url":"https://www.synapse.org/#!Synapse:syn7364923, https://www.synapse.org/#!Synapse:syn7118450","dataSubType":"simple somatic mutation (SNVs and indels)","label":"consensus coding mutations","name":"October_2016_whitelist_2583.snv_mnv_indel.maf.coding.xena","wrangling_procedure":"download maf file, then cut -f 1,2,3,4,6,8,10,13,29,38,39 October_2016_whitelist_2583.snv_mnv_indel.maf, averaged VAF (MNVs have multiple VAF, one for each base call), mapped to donor ids, selected only coding mutations, about 0.5% of all mutations calls.","assembly":"hg19","type":"mutationVector","version":"2017-01-21","description":"PCAWG-1 working group data. Consensus SNVs and indels, coding mutations only. 2778 whitelisted samples from 2583 whitelisted donors. Note that adjacent SNVs have been merged into MNVs in this MAF."}

simple somatic mutation (SNVs and indels)

{"name":"gencode.annotation.gene.probemap","type":"probeMap","version":"2016-05-05","assembly":"hg19","xdb":"genecode Release 19 (GRCh37.p13)","note":"derived from v19, gencode.v19.annotation.gene.probemap"}

{"cohort":"PCAWG (donor centric)","url":"https://www.synapse.org/#!Synapse:syn7221157, https://www.synapse.org/#!Synapse:syn5383480, https://www.synapse.org/#!Synapse:syn2364711","probeMap":"gencode.annotation.gene.probemap","dataSubType":"gene fusion RNAseq","label":"gene-level fusion","name":"pcawg3_fusions_PKU_EBI.gene_centric.donor.xena","wrangling_procedure":"Donwload data pcawg3_fusions_PKU_EBI.gene_centric.tsv.gz, only select tumor data, mapped to donor id, when multiple tumors are available per donor, avarage of the fusion calls (0,1) are used as the value for the donor.","type":"genomicMatrix","version":"2017-02-22","unit":"binary fusion call, 1 fusion, 0 otherwise","description":"PCAWG-3 gene fusion calls (tumors only). Binary gene-level fusion call, 1 fusion, 0 otherwise. Merged calls from EBI-EMBL and PKU groups"}

{"cohort":"PCAWG (donor centric)","url":"https://www.synapse.org/#!Synapse:syn7596712, https://www.synapse.org/#!Synapse:syn5964535","dataSubType":"structural somatic mutation (structural variant)","label":"merge set v 1.6","name":"pcawg_consensus_1.6.161116.somatic_svs.xena.donor","wrangling_procedure":"Vcf files (.somatic_svs.tar.gz) are downloaded from Synapse, wrangled into UCSC Xena format for structrual variant dataset, breakpoint genes are assigned by the Xena team if the breakpoint (svtype=BND in the vcf file) overlaps the gene region plus 2kb upstream of Tx start. Aliquot_id (uuid) is mapped to ICGC donor id in the dataset.","assembly":"hg19","customcolor":{"description":{"url":"https://docs.google.com/spreadsheets/d/17zFEZIs4y1oD_gjYLXZGlFOpxxNmqpMr-UKIG-X1nMk/edit"},"SV":{"9":"#DC85EE","3":"#F7F797","22":"#9E2800","4":"#7C749B","8":"#96D53D","14":"#336C80","21":"#E0BD8C","20":"#475ECC","19":"#F88B78","17":"#D4C5F2","Y":"#B6EBEA","15":"#F7CA44","7":"#DC8747","5":"#E85726","18":"#995493","12":"#78AAF1","13":"#D9C6CA","6":"#B395F8","1":"#DE47AB","X":"#F2BBD2","11":"#88DB68","2":"#72BE97","16":"#32C7C7","10":"#7D32B3"}},"type":"mutationVector","version":"2017-01-18","description":"<b>PCAWG6 Structural Variant merge set v 1.6.</b><br><br>Merge is based on SV calls from BRASS (Sanger), DELLY (EMBL-DKFZ), dRanger and SNOWMAN (BROAD). This dataset is the filtered somatic SV calls (.somatic_svs.tar.gz). Breakpoint gene assignment: gene region plus 2kb upstream of Tx start of the gene."}