In:
Bioinformatics, Oxford University Press (OUP), Vol. 33, No. 15 ( 2017-08-01), p. 2322-2329
Abstract:
Accurate identification of genotypes is an essential part of the analysis of genomic data, including in identification of sequence polymorphisms, linking mutations with disease and determining mutation rates. Biological and technical processes that adversely affect genotyping include copy-number-variation, paralogous sequences, library preparation, sequencing error and reference-mapping biases, among others. Results We modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models. In most cases the best model was comprised of two distributions. The major-component distribution is similar to a binomial distribution with low error and low reference bias. The minor-component distribution is overdispersed with higher error and reference bias. We also found that sites fitting the minor component are enriched for copy number variants and low complexity regions, which can produce erroneous genotype calls. By removing sites that do not fit the major component, we can improve the accuracy of genotype calls. Availability and Implementation Methods and data files are available at https://github.com/CartwrightLab/WuEtAl2017/ (doi:10.5281/zenodo.256858). Supplementary information Supplementary data is available at Bioinformatics online.
Type of Medium:
Online Resource
ISSN:
1367-4803
,
1367-4811
DOI:
10.1093/bioinformatics/btx133
Language:
English
Publisher:
Oxford University Press (OUP)
Publication Date:
2017
detail.hit.zdb_id:
1468345-3
SSG:
12
