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The variant call format and VCFtools

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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, 1000 Genomes Project Analysis Group·2011·Bioinformatics

DOI 10.1093/bioinformatics/btr330

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Abstract

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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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Self-citation
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877

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Authors: Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., McVean, G., Durbin, R., & 1000 Genomes Project Analysis Group
Venue: Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2011-06-07
Volume: 27
Issue: 15
Pages: 2156-2158
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/btr330
OpenAlex: W2149992227
Cited by: 16,200
References: 2
FWCI: 52.43
Type: journal article
Language: en
Open access: hybrid

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