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Genotype and SNP calling from next-generation sequencing data

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Nielsen, Rasmus, Paul, Joshua S., Albrechtsen, Anders, Song, Yun S.·2011·Nature Reviews Genetics

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Abstract

Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies.

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Authors: Nielsen, R., Paul, J. S., Albrechtsen, A., & Song, Y. S.
Affiliations: University of California, Berkeley (US)
University of Copenhagen (DK)
Corresponding author: Nielsen, Rasmus
Song, Yun S.
ORCID: Nielsen, Rasmus
Paul, Joshua S.
Albrechtsen, Anders
Song, Yun S.
Venue: Nature Reviews Genetics
Publisher: Springer Science and Business Media LLC
Published: 2011-05-18
Volume: 12
Issue: 6
Pages: 443-451
ISSN: 1471-0056 (ISSN-L)
1471-0064
DOI: 10.1038/nrg2986
PMC: PMC3593722
OpenAlex: W2131016694
Cited by: 1,396
References: 57
Citations by year: 2026: 35 · 2025: 45 · 2024: 72 · 2023: 51 · 2022: 87 · 2021: 79 · 2020: 98 · 2019: 104 · 2018: 99 · 2017: 99 · 2016: 131 · 2015: 114 · 2014: 151 · 2013: 119 · 2012: 90
FWCI: 11.06
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature Reviews Genetics (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
Funders: National Science Foundation
National Institutes of Health
National Human Genome Research Institute (R01HG003229, R01-HG003229-0551, T32HG00047, T32HG000047, R01-HG003229-05)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords: genotype calling, SNP calling, next-generation sequencing, low-pass sequencing, uncertainty quantification, genotyping accuracy
MeSH terms: Alleles, Chromosome Mapping, Data Interpretation, Statistical, Genotype, Humans, Probability, Linkage Disequilibrium, Likelihood Functions, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Genetic Diseases, Inborn

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Genotype and SNP calling from next-generation sequencing data

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