{"cohort":"PCAWG (specimen centric)","url":"https://www.synapse.org/#!Synapse:syn8145655","probeMap":"JuncBASE_alternative_donor.probeMap","dataSubType":"alternative splicing events","label":"JuncBASE - alternative donor exon-exon junction","name":"JuncBASE_alternative_donor.sp.xena","type":"genomicMatrix","version":"2017-03-22","unit":"percent of junction inclusion","description":"Start and end coordinates are exon-exon junction positions. Alternative donor exon-exon junction inclusion estimated by the JuncBASE method. 100.0 means 100% exon inclusion."}

{"cohort":"PCAWG (specimen centric)","url":"https://www.synapse.org/#!Synapse:syn8145655","probeMap":"JuncBASE_cassette.probeMap","dataSubType":"alternative splicing events","label":"JuncBASE - exon skipping","name":"JuncBASE_cassette.sp.xena","type":"genomicMatrix","version":"2017-03-22","unit":"percent of exon inclusion","description":"cassette exon inclusion estimated by the JuncBASE method. 100 means 100% exon inclusion means (i.e. no exon skipping). 0 means 0% exon inclusion (i.e. the exon is completely skipped)."}

{"cohort":"PCAWG (specimen centric)","url":"https://www.synapse.org/#!Synapse:syn8145655","probeMap":"JuncBASE_intron_retention.probeMap","dataSubType":"alternative splicing events","label":"JuncBASE - intron retention","name":"JuncBASE_intron_retention.sp.xena","type":"genomicMatrix","version":"2017-03-22","unit":"percent of intron retention","description":"Intron retention inclusion estimated by the JuncBASE method. 100.0 means 100% retention."}

{"cohort":"PCAWG (specimen centric)","url":"https://www.synapse.org/#!Synapse:syn7364924, https://www.synapse.org/#!Synapse:syn7118450","dataSubType":"simple somatic mutation (SNVs and indels)","label":"consensus coding mutations","name":"October_2016_all_patients_2778.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_all_patients_2778.snv_mnv_indel.maf, mapped to specimen ids, averaged VAF (MNVs have multiple VAF, one for each base call), selected only coding mutations, about 0.8% 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."}