>Variant discovery The GATK (McKenna et al. 4)) HaplotypeCaller estimates the most likely genotypes and allele frequencies in an alignment using a Bayesian likelihood model for every position of the genome regardless of whether a variant was detected at that site or not. This information can later be used in the project based genotyping step. A joint analysis has been performed of all the samples in the project. This leads to a posterior probability of a variant allele at a site. SNPs and small Indels are written to a VCF file, along with information such as genotype quality, allele frequency, strand bias and read depth for that SNP/Indel. Based on quality thresholds from the GATK "best practices" (Van der Auwera et al. 5)) the SNPs and indels are filtered and marked as Lowqual or Pass resulting in a final VCF file.