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GATK
The Genome Analysis Toolkit (GATK) is the standard variant caller after BWA alignment.
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.
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 43(5): 491-8.