HaplotypeCaller
HaplotypeCaller is a variant-calling tool in the Genome Analysis Toolkit (GATK) developed by the Broad Institute. It detects single nucleotide variants (SNVs) and small insertions and deletions (indels) from mapped sequencing reads by reconstructing possible haplotypes in local genomic regions and evaluating their likelihood given the observed read data.
The algorithm identifies "active regions" with evidence of variation, performs local de novo assembly (using de
HaplotypeCaller is widely used in human and non-human genomics due to its improved handling of indels and
Limitations include increased computational and memory demands relative to lightweight callers, potential sensitivity to read mapping