Use of VQSR when joint calling samples from targeted and whole genome sequencing

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Scott Frodsham

• July 02, 2020 17:40

I'm interested in joint calling samples obtained through targeted sequencing and whole genome sequencing. Can anyone help me understand whether hard filtering or VQSR is most appropriate in this case? I understand that hard filtering is best for targeted sequencing and for whole exome sequencing with fewer than 30 samples, but what I want to do isn't so clear cut as either of those options.

Any insight would be helpful.

Thanks so much,

Scott Frodsham

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  Genevieve Brandt (she/her)

  • July 02, 2020 20:48

  Hi ,

  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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