Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing.

ABSTRACT:

Background

Compared to classical genotyping, targeted next-generation sequencing (tNGS) can be custom-designed to interrogate entire genomic regions of interest, in order to detect novel as well as known variants. To bring down the per-sample cost, one approach is to pool barcoded NGS libraries before sample enrichment. Still, we lack a complete understanding of how this multiplexed tNGS approach and the varying performance of the ever-evolving analytical tools can affect the quality of variant discovery. Therefore, we evaluated the impact of different software tools and analytical approaches on the discovery of single nucleotide polymorphisms (SNPs) in multiplexed tNGS data. To generate our own test model, we combined a sequence capture method with NGS in three experimental stages

SUBMITTER: Elsharawy A 

PROVIDER: S-EPMC3563481 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature