GATK

Developed by the Broad Institute, the Genome Analysis Toolkit (GATK) first calls raw variants for each sample read. Then GATK analyzes the variants against known variants, and applies a calibration procedure to compute a false discovery rate for each variant. Variants are flagged as homozygous (1/1) or heterozygous (0/1) in the VCF file sample column.

The GATK best practices were guidelines for the app; they are described here: www.broadinstitute.org/gatk/guide/topic?name=best-practices

For more information about GATK, see www.broadinstitute.org/gatk and www.broadinstitute.org/gatk/about/citing-gatk.