Consistency of the site with strictly two segregating haplotypes
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.
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.
GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA