Documentation

HaplotypeScore

Consistency of the site with two (and only two) segregating haplotypes.

Category Variant Annotations

VCF Field INFO (variant-level)

Type StandardAnnotation, ActiveRegionBasedAnnotation


Overview

Higher scores are indicative of regions with bad alignments, often leading to artifactual SNP and indel calls. Note that the Haplotype Score is only calculated for sites with read coverage.

See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36. GTD: NA