An empirical Bayes method for genotyping and SNP detection using multi-sample next-generation sequencing data Article Swipe
Gongyi Huang
,
Shaoli Wang
,
Xueqin Wang
,
Na You
·
YOU?
·
· 2016
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btw409
YOU?
·
· 2016
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btw409
Motivation: The development of next generation sequencing technology provides an efficient and powerful approach to rare variant detection. To identify genetic variations, the essential question is how to quantity the sequencing error rate in the data. Because of the advantage of easy implementation and the ability to integrate data from different sources, the empirical Bayes method is popularly employed to estimate the sequencing error rate for SNP detection. Results: We propose a novel statistical model to fit the observed non-reference allele frequency data, and utilize the empirical Bayes method for both genotyping and SNP detection, where an ECM algorithm is implemented to estimate the model parameters. The performance of our proposed method is investigated via simulations and real data analysis. It is shown that our method makes less genotype-call errors, and with the parameter estimates from the ECM algorithm, it attains high detection power with FDR being well controlled. Availability and implementation : The proposed algorithm is wrapped in the R package ebGenotyping, which can be downloaded from http://cran.r-project.org/web/packages/ebGenotyping/ . Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bioinformatics/btw409
- https://academic.oup.com/bioinformatics/article-pdf/32/21/3240/7889696/btw409.pdf
- OA Status
- bronze
- Cited By
- 5
- References
- 24
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2471838566
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W2471838566Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/bioinformatics/btw409Digital Object Identifier
- Title
-
An empirical Bayes method for genotyping and SNP detection using multi-sample next-generation sequencing dataWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2016Year of publication
- Publication date
-
2016-07-04Full publication date if available
- Authors
-
Gongyi Huang, Shaoli Wang, Xueqin Wang, Na YouList of authors in order
- Landing page
-
https://doi.org/10.1093/bioinformatics/btw409Publisher landing page
- PDF URL
-
https://academic.oup.com/bioinformatics/article-pdf/32/21/3240/7889696/btw409.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
bronzeOpen access status per OpenAlex
- OA URL
-
https://academic.oup.com/bioinformatics/article-pdf/32/21/3240/7889696/btw409.pdfDirect OA link when available
- Concepts
-
Bayes' theorem, Computer science, Genotyping, Data mining, Sample size determination, Word error rate, Statistical power, SNP genotyping, Statistics, Bayesian probability, Genotype, Artificial intelligence, Mathematics, Biology, Genetics, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
5Total citation count in OpenAlex
- Citations by year (recent)
-
2024: 1, 2019: 1, 2017: 3Per-year citation counts (last 5 years)
- References (count)
-
24Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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