Genotype and SNP calling from next-generation sequencing data

An overview of the steps required in converting next-generation sequencing (NGS) data into accurate called SNPs and genotypes, a process that is crucial for the many downstream analyses of NGS 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.