DRAGEN-GATK: how to create gvcfs

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Katherine Fawcett

• March 27, 2024 12:53

Hello!

I would like to use the DRAGEN-GATK workflow to create a gvcfs.  When I run the workflow described here ((How to) Run germline single sample short variant discovery in DRAGEN mode – GATK (broadinstitute.org)) on a single sample, the output appears to be a standard vcf without information on non-variant sites.

I'm using gatk version 4.4.0.0.

Many thanks,

Kath

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  James Emery

  • April 01, 2024 16:57

  Hello Katherine Fawcett. If you want the GATK to output a GVCF you use the extra flag `--ERC GVCF` which makes the HaplotypeCaller produce a GVCF instead of a VCF. This is compatible with `--dragen-mode` but it is not part of the official tested pathway for DRAGEN-GATK so it is not as strongly guaranteed that the annotations for the non-variant sites will match with DRAGEN annotations. 

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  Katherine Fawcett

  • April 04, 2024 14:52

  Thanks very much, James.  Do you know if this will be made part of the official DRAGEN-GATK pipeline at some point?

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