Largest contiguous homopolymer run of the variant allele
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 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA