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How can I know if something went wrong during assembly?

GennadyGennady RussiaMember

I'm running HaplotypeCaller with default options (no force-active, no disable-optimizations) and want to distinguish two cases:

1) HC does not call variant because it successfully assembled the area around and see no evidence for variant
2) HC gave up assembling hard region or got an assemly which does not cover expected SNP location etc

I know I can use -force-active + disable-optimizations to produce bamout and parse it to compute coverage, but HC is quite slow without optimizations... Is there a simple and fast way?

Thank you in advance!


  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @Gennady ,

    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, see this announcement and check out our support policy.

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