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Genotype and SNP calling from next-generation sequencing data
Open accessAbstract
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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“Similarly, NGS technology has been used to call SNP genotypes and structural variations and provides the ultimate coverage and resolution of genetic variations including private mutations of individuals.”
From Integrative Analysis of Multi-omics Data for Discovery and Functional Studies of Complex Human Diseases (2016) · cites this paper as Nielsen et al., 2011
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Metadata
- 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.
- Venue
- Nature Reviews Genetics
- Published
- 2011-05-18
- Volume
- 12
- Issue
- 6
- Pages
- 443-451
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- 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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