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A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar

Garrison, Erik ; Kronenberg, Zev N ; Dawson, Eric T ; Pedersen, Brent S ; Prins, Pjotr Schneidman-Duhovny, Dina

PLoS computational biology, 2022-05, Vol.18 (5), p.e1009123-e1009123 [Periódico revisado por pares]

United States: Public Library of Science

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Título:
A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar
Autor: Garrison, Erik ; Kronenberg, Zev N ; Dawson, Eric T ; Pedersen, Brent S ; Prins, Pjotr
Schneidman-Duhovny, Dina
Assuntos: Analysis ; Annotations ; Application programming interface ; Best practice ; Bioinformatics ; Biology and Life Sciences ; C plus plus ; Chromosomes ; Computational Biology ; Computer and Information Sciences ; Computer software industry ; Deoxyribonucleic acid ; DNA ; Ecosystem ; Engineering and Technology ; Format ; Freeware ; Gene mutations ; Genetic Variation - genetics ; Genomes ; Genomics ; Graphical representations ; Libraries ; Methods ; Mutation ; Nucleotides ; Open source software ; Population genetics ; Population studies ; Programming languages ; Public domain ; Public software ; Research and Analysis Methods ; RNA ; RNA processing ; Software ; Software development tools ; Software utilities
É parte de: PLoS computational biology, 2022-05, Vol.18 (5), p.e1009123-e1009123
Notas: new_version
ObjectType-Article-1
SourceType-Scholarly Journals-1
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The authors have declared that no competing interests exist.
Descrição: 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. The VCF format can represent single nucleotide variants, multi-nucleotide variants, insertions and deletions, and simple structural variants called and anchored against a reference genome. Here we present a spectrum of over 125 useful, complimentary free and open source software tools and libraries, we wrote and made available through the multiple vcflib, bio-vcf, cyvcf2, hts-nim and slivar projects. These tools are applied for comparison, filtering, normalisation, smoothing and annotation of VCF, as well as output of statistics, visualisation, and transformations of files variants. These tools run everyday in critical biomedical pipelines and countless shell scripts. Our tools are part of the wider bioinformatics ecosystem and we highlight best practices. We shortly discuss the design of VCF, lessons learnt, and how we can address more complex variation through pangenome graph formats, variation that can not easily be represented by the VCF format.
Editor: United States: Public Library of Science
Idioma: Inglês

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A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar

Garrison, Erik ; Kronenberg, Zev N ; Dawson, Eric T ; Pedersen, Brent S ; Prins, Pjotr Schneidman-Duhovny, Dina

United States: Public Library of Science

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