# HaplotypeScore

Consistency of the site with strictly two segregating haplotypes

## Overview

For diploid organisms, barring chromosomal abnormalities, we expect that any given sample has no more than 2 segregating haplotypes at a given site. If there is evidence for more than 2 segregating haplotypes, the read data should be considered suspect and the evidence artifactual. Higher scores are indicative of regions with bad alignments, typically leading to artifactual SNP and indel calls.

### Caveats

HaplotypeCaller does not output this annotation because it already evaluates haplotype segregation internally. This annotation is only informative (and available) for variants called by Unified Genotyper.