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Should reference sequence surrounding homopolymer warning site show a long repetitive sequence?
I am using Variant Annotator to annotate my vcf. One of the annotations is Homopolymers run - I get several error messages like the one below regarding homopolymers. I have looked at the reference sequence for some of these positions and I don't see a long homopolymer run in the sequence. Should I be seeing a long homopolymers in the reference? Thanks for clarifying. I am using GATK 3.6.
WARN 15:58:23,128 HomopolymerRun - Encountered a homopolymer at 10:118927198 longer than the tool's default window size, so the position was skipped. To process this position, add --reference_window_stop to your command with a value equal or greater than 79