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Published November 5, 2016 | Version v1.6.11
Software Open

mskcc/vcf2maf: vcf2maf v1.6.11

Authors/Creators

  • 1. Memorial Sloan Kettering Cancer Center
  • 2. MSKCC
  • 3. OHSU

Description

  • Added a data/hg19_to_GRCh37.chain for use with vcf2maf --remap-chain, to simplify lives of users handling hg19 VCFs. Notice how only chrM➜MT needs genomic loci remapping, while all others just need renaming.
  • Better handling of ExAC allele counts, without needing VEP's ExAC plugin. See #90, #91, #37 for details.
  • Now using ExAC subpopulation allele counts for FILTER tag common_variant, instead of allele frequencies.
  • So the common_variant tag is now redefined as: If allele count across at least one ExAC subpopulation (AFR AMR EAS FIN NFE OTH SAS) is >16, and ClinVar doesn't say it's pathogenic.
  • The maximum subpopulation allele count is also configurable with --max-filter-ac, defaulting to 16. The ExAC VCF can also be swapped out with the gnomAD VCF, when it's released, using argument --filter-vcf.
  • Other minor fixes

Files

mskcc/vcf2maf-v1.6.11.zip

Files (2.8 MB)

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md5:05d5a8337a74fb4a42922c7623390668
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Additional details

Related works

Is supplement to
https://github.com/mskcc/vcf2maf/tree/v1.6.11 (URL)