Identify homopolymer stretches in a given genome

Question

[ATpoint]

Is anyone aware of an implementation that identifies or blacklists homopolymer stretches in a given genome/fasta, lets say with a length of 6 or greater?

Answer 1

[Pierre Lindenbaum]

There is a module HomopolymerRun in GATK Variant Annotation: see https://software.broadinstitute.org/gatk/gatkdocs/3.8-0/org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotator.php and https://software.broadinstitute.org/gatk/gatkdocs/3.8-0/org_broadinstitute_gatk_tools_walkers_annotator_HomopolymerRun.php

I've also written a VCFPolyX: http://lindenb.github.io/jvarkit/VCFPolyX.html