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Query about wgs_calling_regions.hg38.interval_list from GRCh38 gatk bundle

Hi GATK team,

We are using wgs_calling_regions.hg38.interval_list from gatk bundle to call variants. Could you please confirm the details about the removed/masked regions from the reference.
Particularly we would like to know about centromere regions inclusion. Thanks.

Regards
Lavanya

Best Answer

Answers

  • LavanyaLavanya Member

    Thanks Bhanu.

  • igorigor New YorkMember ✭✭
    edited December 2019

    Can you clarify what HG38excludeNs.interval_list and genome.interval_list are and/or where they come from?

    I assume that HG38excludeNs.interval_list is the full genome without the N bases and genome.interval_list is the full genome. When you intersect them, wouldn't you just get HG38excludeNs.interval_list?

  • 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”).

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