vcf2maf v1.6.12

• Added whitelist of known somatic events, to be removed from the ExAC VCF during VEP install.
• ExAC-based filtering cutoff is now tightened from AC>16 to AC>10.
• ClinVar is no longer a whitelist for ExAC-based filter.
• Other minor fixes.

vcf2maf v1.6.11

• 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

• 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

• 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

• 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

• 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

• Hotfix in vcf2maf for missing AD values and incorrect GT
• Hotfix in vcf2vcf for incorrect GT

vcf2maf v1.6.5

• 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

• 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

• 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