Genotype and SNP calling from next-generation sequencing data

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.