A framework for variation discovery and genotyping using next-generation DNA sequencing data.

ABSTRACT: Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. The amounts of raw data produced are prodigious, and many computational steps are required to translate this output into high-quality variant calls. We present a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs. Our process includes (i) initial read mapping; (ii) local realignment around indels; (iii) base quality score recalibration; (iv) SNP discovery and genotyping to find all potential variants; and (v) m

SUBMITTER: DePristo MA 

PROVIDER: S-EPMC3083463 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature