Quantifying single nucleotide variant detection sensitivity in exome sequencing.

ABSTRACT:

Background

The targeted capture and sequencing of genomic regions has rapidly demonstrated its utility in genetic studies. Inherent in this technology is considerable heterogeneity of target coverage and this is expected to systematically impact our sensitivity to detect genuine polymorphisms. To fully interpret the polymorphisms identified in a genetic study it is often essential to both detect polymorphisms and to understand where and with what probability real polymorphisms may have been missed.

Results

Using down-sampling of 30 deeply sequenced exomes and a set of gold-standard single nucleotide variant (SNV) genotype calls for each sample, we developed an empirical model relating the read depth at a polymorphic site to the probability of calling the correct genotype at

SUBMITTER: Meynert AM 

PROVIDER: S-EPMC3695811 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature