Ancestry-agnostic estimation of DNA sample contamination from sequence reads.

ABSTRACT: Detecting and estimating DNA sample contamination are important steps to ensure high-quality genotype calls and reliable downstream analysis. Existing methods rely on population allele frequency information for accurate estimation of contamination rates. Correctly specifying population allele frequencies for each individual in early stage of sequence analysis is impractical or even impossible for large-scale sequencing centers that simultaneously process samples from multiple studies across diverse populations. On the other hand, incorrectly specified allele frequencies may result in substantial bias in estimated contamination rates. For example, we observed that existing methods often fail to identify 10% contaminated samples at a typical 3% contamination exclusion threshold when genetic

SUBMITTER: Zhang F 

PROVIDER: S-EPMC7050530 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature