{"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":"whole genome mutations (non-US donors)","name":"October_2016_whitelist_2583.snv_mnv_indel.maf.xena.nonUS","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, extracted only data from the non-US donors","assembly":"hg19","type":"mutationVector","version":"2017-07-25","description":"<h2>PCAWG-1 Consensus Pass-Only Somatic Whole Genome Mutation Calls for non-US donors</h2>Only 1 representative tumor from multi-tumor donors, hence 2583 samples from 2583 donors; further limit to non-US donors, hence 1782 donors<h3>SNVs</h3>Consensus strategy: a \"2+ of 4\" strategy, taking the union callset of the passing variants from the three core callers (Sanger, Broad, DKFZ-EMBL), plus MuSE 1.0, and filtering out calls made by only one caller.<br><h4>Filters</h4><ul><li>A filter to exclude potential oxidative artifacts</li><li>A filter to exclude calls likely due to PCR or sequencing bias</li><li>A filter that removes calls that are not robust under a different mapping procedure</li><li>A filter that removes calls that are seen in an improved and expanded panel of normals, including germline calls from the PCAWG cases</li><li>A filter that removes SNVs that overlap with germline indels</li><li>Calls that are suspected of being in 1000-genomes and are not sufficiently well supported.</li><li>Calls made on chromosome Y in female donors were removed</li></ul><br><h3>Indels</h3>Consensus strategy: a \"Stacked Logistic Regression\" method where each core caller's \"vote\" for the call is weighted by how it has performed on calls with similar features (read counts, presence in various databases, etc.) was used. The core callers for the Indel calls were the Sanger, DKFZ-EMBL, and BSC SMuFin pipelines.<br><h4>Filters</h4><ul><li>The threshold for a call to pass the consensus model was increased, filtering out marginal calls</li><li>The panel of normal filter </li><li>Calls made on chromosome Y in female donors were removed</li></ul>"}