The variant call format and VCFtools

Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range o...

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Autores principales: Danecek, Petr, Auton, Adam, Abecasis, Goncalo, Albers, Cornelis A., Banks, Eric, DePristo, Mark A., Handsaker, Robert E., Lunter, Gerton, Marth, Gabor T., Sherry, Stephen T., McVean, Gilean, Durbin, Richard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137218/
https://www.ncbi.nlm.nih.gov/pubmed/21653522
http://dx.doi.org/10.1093/bioinformatics/btr330
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author Danecek, Petr
Auton, Adam
Abecasis, Goncalo
Albers, Cornelis A.
Banks, Eric
DePristo, Mark A.
Handsaker, Robert E.
Lunter, Gerton
Marth, Gabor T.
Sherry, Stephen T.
McVean, Gilean
Durbin, Richard
author_facet Danecek, Petr
Auton, Adam
Abecasis, Goncalo
Albers, Cornelis A.
Banks, Eric
DePristo, Mark A.
Handsaker, Robert E.
Lunter, Gerton
Marth, Gabor T.
Sherry, Stephen T.
McVean, Gilean
Durbin, Richard
author_sort Danecek, Petr
collection PubMed
description Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. Availability: http://vcftools.sourceforge.net Contact: rd@sanger.ac.uk
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spelling pubmed-31372182011-07-15 The variant call format and VCFtools Danecek, Petr Auton, Adam Abecasis, Goncalo Albers, Cornelis A. Banks, Eric DePristo, Mark A. Handsaker, Robert E. Lunter, Gerton Marth, Gabor T. Sherry, Stephen T. McVean, Gilean Durbin, Richard Bioinformatics Applications Note Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. Availability: http://vcftools.sourceforge.net Contact: rd@sanger.ac.uk Oxford University Press 2011-08-01 2011-06-07 /pmc/articles/PMC3137218/ /pubmed/21653522 http://dx.doi.org/10.1093/bioinformatics/btr330 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Danecek, Petr
Auton, Adam
Abecasis, Goncalo
Albers, Cornelis A.
Banks, Eric
DePristo, Mark A.
Handsaker, Robert E.
Lunter, Gerton
Marth, Gabor T.
Sherry, Stephen T.
McVean, Gilean
Durbin, Richard
The variant call format and VCFtools
title The variant call format and VCFtools
title_full The variant call format and VCFtools
title_fullStr The variant call format and VCFtools
title_full_unstemmed The variant call format and VCFtools
title_short The variant call format and VCFtools
title_sort variant call format and vcftools
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137218/
https://www.ncbi.nlm.nih.gov/pubmed/21653522
http://dx.doi.org/10.1093/bioinformatics/btr330
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