Genome Analysis Toolkit 1 article

GATK variant discovery gives Genome Analysis Toolkit its role as a genomic variant-analysis toolkit in modern bioinformatics. Researchers use it to handle HaplotypeCaller germline variant calling alongside Mutect2 somatic variant calling, with base quality score recalibration supporting variant quality score recalibration in the same pipeline. GATK focuses on genomic variant-analysis pipelines; alignment tools such as BWA and Bowtie usually operate upstream of its variant-calling steps.