illumina instruments have built-in -or online- analysis software for variant analysis (CASAVA). This software can filter out the false positive variants near the homopolymer repeats (AAAAAAAA) and filter them with "R8" tag.
Is it possible to make homopolymer repeat filter without using illumina's own pipeline? (with another software?)
P.S I noticed that, GATK have HomopolymerRun script that makes similar job. But it is no longer supported and recommended.
Edit: I posted same question on StackExchange. However, I couldn't find answer yet.