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SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data
Open accessAbstract
We present a statistical framework for estimation and application of sample allele frequency spectra from New-Generation Sequencing (NGS) data. In this method, we first estimate the allele frequency spectrum using maximum likelihood. In contrast to previous methods, the likelihood function is calculated using a dynamic programming algorithm and numerically optimized using analytical derivatives. We then use a bayesian method for estimating the sample allele frequency in a single site, and show how the method can be used for genotype calling and SNP calling. We also show how the method can be extended to various other cases including cases with deviations from Hardy-Weinberg equilibrium. We evaluate the statistical properties of the methods using simulations and by application to a real data set.
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“due to the error rate of sequencing, the mixture of nonparenchymal cells and polyploidy of hepatocytes, this approach could not detect low-frequency single-nucleotide polymorphisms in hepatocytes11.”
From Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype (2014) · cites this paper as [11]
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ANGSD: Analysis of Next Generation Sequencing Data
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Metadata
- Authors
- Nielsen, R., Korneliussen, T., Albrechtsen, A., Li, Y., & Wang, J.
- Affiliations
- BGI Group (China) (CN)
- University of Copenhagen (DK)
- Corresponding author
- Nielsen, Rasmus
- Wang, Jun
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-07-24
- Volume
- 7
- Issue
- 7
- Pages
- e37558
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3404070
- OpenAlex
- W2005287518
- Cited by
- 424
- References
- 39
- Citations by year
- 2026: 24 · 2025: 18 · 2024: 43 · 2023: 33 · 2022: 38 · 2021: 40 · 2020: 25 · 2019: 19 · 2018: 37 · 2017: 30 · 2016: 39 · 2015: 30 · 2014: 25 · 2013: 19 · 2012: 1
- FWCI
- 9.58
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Figshare (submittedVersion, cc-by)
- Funders
- Villum Fonden (00007171)
- National Institutes of Health
- National Human Genome Research Institute (R01HG003229)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- allele frequency estimation, allele frequency spectrum, SNP calling, genotype calling, next-generation sequencing, maximum likelihood estimation, Hardy-Weinberg equilibrium, genetic variation
- MeSH terms
- Algorithms, Bayes Theorem, Computer Simulation, Denmark, Gene Frequency, Genotype, Humans, ROC Curve, Software, Likelihood Functions, Computational Biology, Internet, Polymorphism, Single Nucleotide, White People, High-Throughput Nucleotide Sequencing, Exome
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