This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
known site for BaseRecalibrator with hg38
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:
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.