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vcf2maf v1.6.13
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@ckandoth ckandoth released this 17 Jun 19:59
v1.6.13
aec89f9
  • 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.
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