Joint Variant Calling of samples coming from different batches (different genome build or target chip)

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Samreen Zafer

• January 28, 2020 23:04

Hi, I've gone through your articles describing the variant calling on cohort samples.
Could you please publish and article describing your experience, best practices, nuances and things to look out for in the results when calling variants from samples from multiple batches, where the sequencing kits/builds don't necessary match.

A simple example would be- I have sequenced a set of case samples on the latest hg38 based kit (ex. SureSelect Exon V7). And I want to call them with publicly available controls (e.g. an older hg19 based capture kit).

Best Wishes.

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  Bhanu Gandham

  • February 03, 2020 21:27

  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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