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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.

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    $\begingroup$ Yes you can do it with perl or awk or other such languages. $\endgroup$ – WYSIWYG Apr 28 '15 at 4:53
  • $\begingroup$ Does it mean that there is no software for such filtration? Should I write my own script? There should be an easier way. $\endgroup$ – Can H. Apr 29 '15 at 6:40
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    $\begingroup$ People have made such scripts. Try this one called prinseq. It runs on perl $\endgroup$ – WYSIWYG Apr 29 '15 at 8:17

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