Where to get homopolymer annotation for human genome ?

Question

[lzy]

I got lots of SNV and Indel somatic mutations from whole genome sequencing data from tumor. And I want to annotate these somatic mutations with whether located in the homopolymer region of human genome. I have already search the ucsc repeatmasker track, and it does not contain homopolymer annotation. I want to know where to download this annotation or how can I calculate the homopolymer of human genome? Thanks !

Answer 1

[Pierre Lindenbaum]

if your input is a VCF file, you can use GATK VariantAnnotator with -A HomopolymerRun

https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_annotator_HomopolymerRun.php

[lzy]

Thank you very much, I will try this method.

[Charles-Alexandre Roy]

@Pierre Lindenbaum, -A HomopolymerRun isn't mentioned in the documentation on the GATK site or when you run "gatk VariantAnnotator --help" on the command line. Do you know what happened to this option or of another method to find all homopolymer regions in the human genome?