Genotype and SNP calling from next-generation sequencing data

Converting next-generation sequencing (NGS) image files into a set of called SNPs involves a number of steps including image analysis, alignment and assembly, SNP calling and genotype calling.Genotype probabilities for a single individual can be calculated from alignments using recalibrated quality scores.SNP calling and genotype calling is best done using information from multiple individuals simultaneously. The pattern of linkage disequilibrium should be used to call SNPs and genotypes when possible.Analyses of low coverage data can proceed by taking uncertainty in the genotype calls into account, rather than assuming any particular genotype call is correct.The methods used for calling SNPs and for taking uncertainty in SNP genotypes into account can have a strong effect on downstream analyses, including association mapping analyses.