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known site for BaseRecalibrator with hg38

Hello,

I'm trying to call Germline SNPs + Indels as following the best practice pipeline with GATK-4.1.4 on hg38.
To run BaseRecalibrator I'm referring the page:
https://gatkforums.broadinstitute.org/gatk/discussion/1247/what-should-i-use-as-known-variants-sites-for-running-tool-x

I found dbSNP and Mills indels in GATK Bundle hg38, but 1KG indels. Do you recommend to use other indel resource instead, such as I found known_indels.vcf in the bundle beta directory.

Thank you!
Hiroko Matsui

Answers

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