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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

How to find or generate common germline variant sites VCF required by GetPileupSummaries



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    David Benjamin

    You can find it in our best practices google bucket.  Depending on your reference, gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf or gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz (the accompanying VCF indices are also there).

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    Antti Koskenalho

    David, thank you very much for confirming this!

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    Dear GATK Team,

    Related to the above query, I can see there are common germline variant sites VCFs for both b37 and hg38 in the GATK Best Practices Google bucket. However, not for hg19.

    I have lifted over the --germline resource from b37 (af-only-gnomad.raw.sites.b37.vcf.gz) to hg19 using LiftoverVcf. However, for the common germline variant sites VCF, would it be recommended to lift over the existing b37 VCF (small_exac_common_3.vcf) to hg19 using LiftoverVcf?

    Is there a method to generate the common germline variant sites VCF directly from the hg19 --germline-resource?

    Thank you for your time and help.

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    Genevieve Brandt (she/her)

    Hi ISmolicz,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

    For context, check out our support policy.

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