Largest contiguous homopolymer run of the variant allele

Category Variant Annotations

VCF Field INFO (variant-level)

Type ExperimentalAnnotation


Calculates the length of the largest contiguous homopolymer run of the variant allele in either direction on the reference.


This can only be computed for bi-allelic sites.

This is an experimental annotation. As such, it is unsupported; we do not make any guarantees that it will work properly, and you use it at your own risk.

This needs to be computed in a more accurate manner. We currently look only at direct runs of the alternate allele adjacent to this position.

See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA