Combine and Genotype GVCF - running time

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@Anna

• November 25, 2020 14:17

Hello. I am analysing 220 human exomes. I am running CombineGVCF, which is taking a lot of time. I know that it is slower than GenomicsDBImport, so I'm combining separately by chromosomes. Still, it has been over a week now and it is not finished yet. Is this normal?

Considering this, I would also like to ask how much time will GenotypeGVCF need?

 

Thank you in advance!

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• Official comment

  

  Genevieve Brandt (she/her)

  • July 28, 2021 01:33
  • Edited

  Hi Anna,

  Is there a reason you are running CombineGVCFs instead of GenomicsDBImport? If you are running with human exomes, GenomicsDBImport would be the superior option because of the speed ups.

  GenotypeGVCFs should be faster than your CombineGVCFs step.

  Best,

  Genevieve

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  Anton Kovalsky

  • November 26, 2020 03:32

  Hi @anna

  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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