How can I remove Indels from a VCF file that are actually microsatellite variants?

Question

[anp375]

I don't have access to the BAM files that were used to generate the VCF. I only have the VCF file.

How do I go through indels in the VCF file and remove sequence repeat variants?

Thanks.

Answer 1

[Pierre Lindenbaum]

Two options: if the positions of the microsat is known, use a BED file of those microsat. e.g:

http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/stsMap.txt.gz

or using GATK https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotator.php and the module HomopolymerRun ( https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_annotator_HomopolymerRun.php )

[anp375]

Thank you. Hopefully I get the BAMs soon.