# HomopolymerRun

Largest contiguous homopolymer run of the variant allele

## Overview

Repetitive sequences such as homopolymers are difficult to map to the reference because they are associated with multiple alignment possibilities. The proximity of a long homopolymer to your variant site increases the chance that reads were mapped incorrectly in the surrounding region and lowers confidence in the call. If there is a homopolymer on either side of a site, this annotation outputs the length of its largest run.

### Caveats

• This can only be computed for bi-allelic sites.
• The calculation only looks at direct runs of the alternate allele adjacent to this position, which is not a very accurate method.
• 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.