Variant detection and genotype calling using Genome Analysis Tool Kit (GATK)

In this lecture, we will describe the variant (SNP and INDEL) detection pipeline used by the 1000 bull genomes project. The pipeline closely follows the Genome Analysis Tool Kit (GATK, Broad Institute) best practises. Tools that are used to process raw sequence reads for individuals and align them to the genome will be described in detail, including a Base Quality Sequence Recalibration step to detect and correct for patterns of systematic errors in the base quality scores. Also, the tools used to detect variants and call genotypes across all samples and then filter variants using a recalibration against known variants, resulting in a dataset that balances precision and sensitivity.