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

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

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.

microsatellite indel

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updated 8.8 years ago by Pierre Lindenbaum

• written 8.8 years ago by anp375

1 answer

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 )

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written 8.8 years ago by Pierre Lindenbaum

Thank you. Hopefully I get the BAMs soon.

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written 8.8 years ago by anp375

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