This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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.
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?
If I decide run all the normal types of a patient, should I call them together by realigntargetcreator to create a general interval?
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?