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Releases: mskcc/vcf2maf

vcf2maf v1.6.12

09 Dec 16:13
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vcf2maf v1.6.11

13 Nov 07:53
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  • 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.

vcf2maf v1.6.10

14 Oct 03:52
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  • Support for VEP v86
  • vcf2maf can liftOver variants before annotation (e.g. From GRCh37 to GRCh38, hg19 to GRCh37)
  • vcf2maf can store annotated VCF in a different folder using new argument --tmp-dir
  • Updates to isoform overrides, in particular for MSKCC's new IMPACT v6 gene panel
  • Other minor fixes

vcf2maf v1.6.9

28 Sep 18:15
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  • Important: Please re-download this release if you grabbed it before Sept 29th, 2016. There was a bug that prevented the scripts from running on MAFs/VCFs with more than 125,000 variants
  • Entrez_Gene_Id will now be filled as best as possible, using an included mapping from ENSG IDs
  • VEP no longer checks for reference allele mismatches, because vcf2maf/maf2vcf will do it anyway
  • VEP now ignores variant allele change, when looking up known dbSNP/COSMIC variants
  • Now added a column for ExAC_AF_Adj

vcf2maf v1.6.8

01 Sep 22:11
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  • Support for VEP v85
  • Consequence is now a comma-delimited list of all possible effects on the canonical isoform
  • Better handling of reference allele mismatches in maf2vcf and vcf2maf
  • New MAF column flanking_bps gives sequence context
  • New MAF columns variant_id and variant_qual for ID and QUAL from a VCF
  • New vcf2maf option --retain-info to retain data from VCF's INFO fields
  • Renamed column STRAND to STRAND_VEP to avoid mix-up with MAF's Strand
  • Added a basic dockerfile
  • Other bug fixes

vcf2maf v1.6.7

09 Jun 20:18
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  • Support for VEP v84
  • New Variant_Classification named Splice_Region equivalent to splice_region_variant defined here. It is also now ranked as a more deleterious effect than Silent (See #44)
  • ExAC subpopulation OTH is excluded from the common_variant filter, cuz it's too small (See #46)
  • Unrecognized effect/biotype will now receive lowest priority, instead of failing with an error
  • Set Hugo_Symbol to Unknown if neither a gene symbol or transcript ID was assigned by VEP
  • Added unit tests for all 4 scripts
  • Other minor fixes

vcf2maf v1.6.6

21 Apr 21:14
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  • Hotfix in vcf2maf for missing AD values and incorrect GT
  • Hotfix in vcf2vcf for incorrect GT

vcf2maf v1.6.5

21 Apr 21:18
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  • Update instructions and defaults to use VEP v83
  • New vcf2vcf tool to create minimalist VCFs compliant with v4.2 specs
  • vcf2vcf can apply some basic allele-depth based filters to VCFs, added to existing FILTER data
  • Fix bug where a proper VCF AD field was overridden by depths in BCOUNT/TIR/RD/etc.
  • All possible issues with POS for complex indels should now be properly handled
  • Minor bug fixes, and handling new SO terms and other exceptions
  • Add --cache-version option to allow use of user-specified annotation cache

vcf2maf v1.6.4

21 Apr 21:18
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  • Handle undefined Tumor_Seq_Allele2
  • More stringent about reference genome mismatches
  • Handle missing ALLELE_NUM when SV_TYPE defined in INFO
  • Retain FILTER data from input VCF
  • Add a filter called common_variant for variants with >0.04% minor allele frequency in any ExAC subpopulation, unless ClinVar says pathogenic, risk_factor, or protective

vcf2maf v1.6.3

01 Nov 23:12
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  • Support for Ensembl VEP v82
  • Adds minor allele fractions from ExAC, except for known somatic calls
  • Use ENST transcript ID in column 1, if HUGO symbol is unavailable
  • Support new Gencode biotypes