stand_call_conf and stand_emit_conf in GATK 4.2.4.1

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M.R-E.H

• January 17, 2022 16:05

Hello,

I have recently switched to use GATK V4 instead of GATK 3. However, I have noticed that the arguments in bold below which I used to use in GATK3 Haplotypecaller are no longer valid in GATK 4
-stand_call_conf 20.0
-stand_emit_conf 20.0
What alternative does GATK 4 provide or are these arguments no longer necessary ?

Thank you very much.

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  Genevieve Brandt (she/her)

  • January 20, 2022 21:32

  Hi M.R-E.H,

  Good to hear that you are making the switch! -stand_call_conf is still in HaplotypeCaller, but the argument can be used as -stand-call-conf. It is shorthand for --standard-min-confidence-threshold-for-calling, which has a default of 30.0.

  -stand_emit_conf was deprecated in 2016 so it is no longer in HaplotypeCaller (it wasn't in the last versions of GATK3 either). You can read more about this change in a blog post here: https://github.com/broadinstitute/gatk-docs/blob/master/blog-2012-to-2019/2016-12-12-Version_highlights_for_GATK_version_3.7.md

  Please let em know if you have further questions.

  Best,

  Genevieve

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