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What is the current recommended practice for interval padding?

In the GATK Best Practices WDL in github, the GenotypeGVCFs commandline does not specify any interval padding via -ip or --interval-padding parameter.

https://github.com/gatk-workflows/gatk4-germline-snps-indels/blob/master/joint-discovery-gatk4.wdl
(as of commit d9fea5462f148ab3a49a177ddd328ede304f4f62).

However, this old guide from 2017 recommends interval padding of 100bp:

https://software.broadinstitute.org/gatk/documentation/article?id=11062

What is the recommended practice for interval padding for HaplotypeCaller and GenotypeGVCFs v4.x?

Best Answer

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi ,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal/erroneous 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, see this [announcement](https://software.broadinstitute.org/gatk/blog?id=24419 “announcement”) and check out our [support policy](https://gatkforums.broadinstitute.org/gatk/discussion/24417/what-types-of-questions-will-the-gatk-frontline-team-answer/p1?new=1 “support policy”).

  • tnsangertnsanger Member

    That helps quite a bit. Thanks!

    A follow up question: is the 500bp interval padding used by GenomicsDBImport in the joint calling best practices WDL meant to cover possible spanning deletions?

  • gauthiergauthier Member, Broadie, Dev ✭✭✭

    Exactly. Then the GenotypeGVCFs command has --only-output-calls-starting-in-intervals to make sure that the calls for abutting intervals are disjoint, i.e. we don't call variants in the padding twice.

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