Next Generation Sequencing of Pooled Samples: Guideline for Variants' Filtering.

ABSTRACT: Sequencing large number of individuals, which is often needed for population genetics studies, is still economically challenging despite falling costs of Next Generation Sequencing (NGS). Pool-seq is an alternative cost- and time-effective option in which DNA from several individuals is pooled for sequencing. However, pooling of DNA creates new problems and challenges for accurate variant call and allele frequency (AF) estimation. In particular, sequencing errors confound with the alleles present at low frequency in the pools possibly giving rise to false positive variants. We sequenced 996 individuals in 83 pools (12 individuals/pool) in a targeted re-sequencing experiment. We show that Pool-seq AFs are robust and reliable by comparing them with public variant databases and in-house SNP-g

SUBMITTER: Anand S 

PROVIDER: S-EPMC5037392 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature