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Published June 17, 2017 | Version v1.6.13
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mskcc/vcf2maf: vcf2maf v1.6.13

Authors/Creators

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

Description

  • Added p14ARF as a canonical isoform for CDKN2A, in addition to p16INK4A.
  • vcf2vcf can now run mpileup on tumor/normal BAMs to populate an input VCF with allele counts.
  • vcf2vcf can parse/edit INFO/FORMAT fields, and also liftOver variants if given a --remap-chain.
  • Added support for cgpPindel and CaVEMan VCFs from Sanger pipelines.
  • Added arg --any-allele to allow mismatched variant alleles, when VEP reports co-located variants.
  • Added arg --buffer-size to control number of variants loaded at a time, dependent on available RAM.
  • Bug Fixed: all_effects column was skipping effects without gene names, like in regulatory regions.
  • Other minor fixes and additions.

Files

mskcc/vcf2maf-v1.6.13.zip

Files (4.5 MB)

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md5:3620606bc912ebb18c95e7bc47b6ded6
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Additional details

Related works

Is supplement to
https://github.com/mskcc/vcf2maf/tree/v1.6.13 (URL)