The industry-standard GATK Best Practices
When you're isolating DNA in the lab, you don't treat the work like isolated, disconnected tasks. Every task is a step in a well-documented protocol, carefully developed to optimize yield, purity and to ensure reproducibility as well as consistency across all samples and experiments. We believe working with the sequencing data should be treated in the same thorough manner.
That's why GATK comes with complete reads-to-results Best Practices workflow recommendations, battle-tested in production at the Broad Institute and optimized to produce the most accurate results with the most computational efficiency.
GATK4 includes Best Practices workflows for all major classes of variants for genomic analysis in gene panels, exomes and whole genomes. In addition to the industry standard GATK Best Practices workflow for germline short variant discovery, GATK4 offers Best Practices workflows for somatic short variants, somatic and germline copy number variants, and structural variation discovery tools are in active development.