The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index.
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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Twort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Васильевич, Б. В., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945688
Twort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Васильевич, Б. В., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945676
Twort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Васильевич, Б. В., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945751
Twort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Васильевич, Б. В., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945727
Twort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Belkin, V. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945754
Twort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Belkin, V. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945679
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Additional file 1 of Genomic variation in captive deer mouse (Peromyscus maniculatus) populations
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Meisner, J., Albrechtsen, A., & Hanghøj, K. (2021) · Figshare · doi:10.6084/m9.figshare.16702945
Self-citationTwort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Belkin, V. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945712
Twort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Belkin, V. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945673
Twort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Belkin, V. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945739
Twort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Belkin, V. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945697
Twort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Belkin, V. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945691
Twort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Belkin, V. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945745
Twort, V., Laine, V. N., Field, K. A., Whiting-Fawcett, F., Ito, F., Reiman, M., Bartonicka, T., Fritze, M., Ilyukha, V. A., Belkin, V. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26945742
Population structure and domestication history of the Javan banteng
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Uckele, K. A., Philbin, C. S., Richards, L. A., Dyer, L. A., Jahner, J. P., & Parchman, T. L. (2026) · Journal of Heredity · doi:10.1093/jhered/esag004
Biswas, A., & Karanth, P. K. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.06.704511
“935 and realSFS (Nielsen et al., 2012).”
Gupta, A., Cao, Y., Liang, J., & Turakhia, Y. (2026) · IEEE International Symposium on High-Performance Computer Architecture (HPCA) · doi:10.1109/hpca68181.2026.11408544
“Early applications include the Needleman-Wunsch algorithm for global alignment [70], followed by local pairwise alignments [28], multiple sequence alignment [29], [30], homology searches [31], [32], whole-genome alignments [33], basecalling [34], variant calling [35], and pangenomics [89], [90].”
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“931 (Nielsen et al. 2012).”
The dynamic genomes of Salvinia reshape our understanding of fern chromosome evolution
Rizzieri, Y. C., Limpanasittichai, P., Hernández, F., Mendez-Reneau, J. I., Holt, S. D., Sutherland, B., Mandáková, T. M., Beck, J. B., Kuo, L., Kooyers, N. J., et al. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2602084123
Habitat discontinuity and fidelity to migratory routes shape narwhal genetic structure and diversityPreprint
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“For the range-wide dataset, we estimated F ST using ANGSD (Nielsen et al. 2012; Korneliussen et al. 2014).”
Crego-Walters, M., Cuadros-Espinoza, S., Ruiz‐Gartzia, I., Han, S., Hermosilla-Albala, N., Helsen, P., Frandsen, P., Prats, A. M. B., Alentorn-Moron, P., Fontsere, C., et al. (2026) · Genome biology · doi:10.1186/s13059-026-04195-8
“C 50 -baq 1 -minMapQ 20 -minQ 20 -setMaxDepth 200 -doCounts 1 -GL 1 -doSaf 1 -r chr21: -out ${ID}_heterozyg | realSFS ${ID}_heterozyg.saf.idx > ${ID}_est.ml [84].”
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“We estimated each individual SFS with realSFS (Nielsen et al. 2012) and computed heterozygosity as the proportion of heterozygous sites over the total number of analysed sites.”
Alaçamlı, E., Sasso, S., Didonna, R., Biagini, S. A., (Urd), I. R., Jonuks, T., Tõrv, M., Valk, H., Kivisild, T., Tambets, K., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.13.744432
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Convergent molecular changes in populations of two pipefish species in the Baltic SeaPreprint
Drewalowski, J. A., Taub, E., Trillo, O., Abashkina, M., Rosenqvist, G., Kliver, S. F., Kovačić, I., Mak, S. S. T., Bogaards, J., Kvarnemo, C., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.23.753463
“Nucleotide diversity (π) per population was calculated for 50,000 base pair sliding windows with a step size of 10,000 bases using thetaStat do_stat from ANGSD (Nielsen et al. 2012), dividing the pairwise theta (tP) by the window size.”
InfluentialGenome-Wide Association Study and Candidate Gene Mining for First Pod Height in Soybean
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“1) [33] using SOAP2 [34], and SNPs were called by RealSFS based on Bayesian estimation of the site frequency [35,36].”
Self-citation
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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