Journal
BIOINFORMATICS
Volume 25, Issue 16, Pages 2074-2075Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btp344
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Funding
- Wellcome Trust
- MRC [G0600805] Funding Source: UKRI
- Medical Research Council [G0600805] Funding Source: researchfish
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Here, we present a method for estimating the frequencies of SNP alleles present within pooled samples of DNA using high-throughput short-read sequencing. The method was tested on real data from six strains of the highly monomorphic pathogen Salmonella Paratyphi A, sequenced individually and in a pool. A variety of read mapping and quality-weighting procedures were tested to determine the optimal parameters, which afforded >= 80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40x, declining only slightly at read depths 20-40x.
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