Largest contiguous homopolymer run of the variant allele
INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
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.
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.