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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?

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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.

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  • 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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