Genotype and SNP calling from next-generation sequencing data

http://www.nature.com/nrg/journal/v12/n6/pdf/nrg2986.pdf

Abstract

Meaningful analysis of next-generation sequencing (NGS) data, which are  produced extensively by genetics and genomics studies, relies crucially on the accurate  calling of SNPs and genotypes. Recently developed statistical methods both improve  and quantify the considerable uncertainty associated with genotype calling, and will  especially benefit the growing number of studies using low- to medium-coverage data.  We review these methods and provide a guide for their use in NGS studies.