vcf2maf v1.6.2

• Handle more types of shitty input formats
• Handle MAFs where a tumor ID was matched to more than 1 normal ID
• Trim reference/variant alleles with more than 1 preceding reference bps

vcf2maf v1.6.1

• Cache contents of per-TN VCFs before writing to disk, instead of opening separate file handles

vcf2maf v1.6

• Support for any of the species that VEP can handle
• Support for snpEff removed (will return when INFO:ANN conventions match VEP)
• Improve speed of maf2vcf and maf2maf by creating/annotating a multi-sample VCF
• Added EAS_MAF and SAS_MAF from 1000g, which changes column ordering
• Additional VEP columns added: IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO

vcf2maf v1.5.4

• Fix issues when ALT alleles are a SNP and indel, both non-REF
• When looking up known variants, match ALT alleles in addition to POS
• Remove --gencode_basic so VEP maps variants to all possible isoforms
• Fix exception that could cause blank t_depth or n_depth

vcf2maf v1.5.3

• Set VEP to shift HGVS indels to 3' end
• Support user-defined isoforms with --custom-enst

vcf2maf v1.5.2

• Changed license from LGPL3 to Apache2
• Support for VEP v79 and some new biotypes and effects
• maf2maf hotfix for non-unique hash keys

vcf2maf v1.5.1

• Update to VEP v78
• Support ref-fasta with lowercase bps
• Support mpileup VCFs
• Avoid forking VEP since it seems slower

vcf2maf v1.5

• New tool maf2maf that runs maf2vcf + vcf2maf, to generate a new MAF with VEP annotations
• Support for MAFs with missing data: reasonable assumptions are made and warnings are shown as necessary
• Add a field named HGVSp_Short, for 1-letter AA codes and other customization
• Minor bugs fixed, exceptions handled, and some backward compatibility added

vcf2maf v1.4

• Updated to use VEP v76, which brings support for GRCh38
• Generalized code to support other reference genomes/species
• Report protein changes with 1-letter AA codes in an extra MAF column
• Report alleles from matched normal in MAF columns 18 and 19
• Report dbSNP rsIDs from VEP in MAF column 14
• Support >1 non-REF variants in tumor and/or normal samples
• If DP (depth) is not in VCF, get it by adding ADs (allele depths)
• Files in the repo have been reorganized more meaningfully
• Much better documentation based on FAQs
• Added test MAFs for maf2vcf
• Other minor bugfixes

vcf2maf v1.3

• Added a maf2vcf helper script
• Support added for many new variant effects
• Several new test VCFs in various simple/complex formats
• Support for extracting ALT/REF depths from various simple/complex VCF formats
• Simple cutoff-based genotype prediction based on ALT/REF depths, if GT is undefined in VCF
• Avoid re-annotation if a .vep.vcf or .snpeff.vcf was generated in a previous run
• Create an output MAF with only a header, when given VCFs with zero variants