Vcflib and tools for processing the VCF variant call format

Abstract

Since its introduction in 2011 the variant call format (VCF) has been widely adopted for processing DNA and RNA variants in practically all population studies — as well as in somatic and germline mutation studies. VCF can present single nucleotide variants, multi-nucleotide variants, insertions and deletions, and simple structural variants called against a reference genome. Here we present over 125 useful and much used free and open source software tools and libraries, part of vcflib tools and bio-vcf. We also highlight cyvcf2, hts-nim and slivar tools. Application is typically in the comparison, filtering, normalisation, smoothing, annotation, statistics, visualisation and exporting of variants. Our tools run daily and invisibly in pipelines and countless shell scripts. Our tools are part of a wider bioinformatics ecosystem and we consider it very important to make these tools available as free and open source software to all bioinformaticians so they can be deployed through software distributions, such as Debian, GNU Guix and Bioconda. vcflib, for example, was installed over 40,000 times and bio-vcf was installed over 15,000 times through Bioconda by December 2020. We shortly discuss the design of VCF, lessons learnt, and how we can address more complex variation that can not easily be represented by the VCF format. All source code is published under free and open source software licenses and can be downloaded and installed from https://github.com/vcflib. Author summary Most bioinformatics workflows deal with DNA/RNA variations that are typically represented in the variant call format (VCF) — a file format that describes mutations (SNP and MNP), insertions and deletions (INDEL) against a reference genome. Here we present a wide range of free and open source software tools that are used in biomedical sequencing workflows around the world today.