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parameter questions for haplotypecaller


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?

Best Answer


  • shenglaishenglai ChicagoMember

    Thank you @Geraldine_VdAuwera !
    iiuc, all normal bams from one patient should be called together through HC so that one patient would only have one gvcf file.
    However, some normal bam files would have some quality issues or contamination problem (like solid tissue normal). Would that impact the results?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Any quality issues or contamination will affect results to some extent. You can do quality control on each bam separately and evaluate whether some are worse than others. Unfortunately we're not able to provide more guidance on that topic.

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