Homopolymeric error sites

praveenrajs

How does GATK2 handle the variants called at homopolymeric regions in the genome? Is this feature enabled and used during the variant calling (with UG/HC) or should we do it separately with VariantFilteration. Is there any specific parameter to control this? Best Raj

Geraldine_VdAuwera

Hi Raj, Currently they are not handled specifically. There is a VariantAnnotator annotation called HRun that looks at homopolymers, but unfortunately it doesn't work very well so we no longer use it in our Best Practices.