GetPileupSummaries common germline variant sites VCF hg38
Answered
Hello,
I am using GATK 4.2.4.1 to perform somatic variant calling. I am trying to perform the filtration of the variants which were called using GetPileupSummaries and CalculateContamination. GetPileupSummaries requires a:
"common germline variant sites VCF, e.g. derived from the gnomAD resource, with population allele frequencies (AF) in the INFO field. This resource must contain only biallelic SNPs and can be an eight-column sites-only VCF. The tool ignores the filter status of the variant calls in this germline resource."
I am looking for this reference VCF file for hg38, for the entire genome, rather than for individual chromosomes. Does this resource exist or is it currently being made?
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Hi Anish K,
I am going to move your post into our Community Discussions -> Documentation Questions topic, as the Somatic topic is for reporting bugs and issues with GATK.
You can read more about our forum guidelines and the topics here: Forum Guidelines.
Best,
Genevieve Brandt
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Hi Anish K,
Yes, we have this resource! I think the answer to your question is here: https://gatk.broadinstitute.org/hc/en-us/community/posts/360067310872-How-to-find-or-generate-common-germline-variant-sites-VCF-required-by-GetPileupSummaries
Please let me know if that doesn't answer your question.
Best,
Genevieve
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