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parameter questions for haplotypecaller

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Hi GATK,

I'm runing the GATK germline variant calling pipeline. I have some questions about realignertargetcreator and haplotypecaller's parameters. Please correct me at any point if I went wrong.

  1. For germline variant calling, if a patient has different types of normal (normal blood, solid tissue normal, etc.), which one should I run haplotypecaller or every type?

  2. If I decide run all the normal types of a patient, should I call them together by realigntargetcreator to create a general interval?

  3. In haplotypecaller, the intervals restrict the active region. However, there's a --forceActive flag in haplotypecaller. I'm just wondering what's the trade off for using --forceActive instead of the intervals. Is the interval kinda like exome capture so that it would work better with WXS?


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