Mutect2 standard-min-confidence-threshold-for-calling

[igordot]

I just tried Mutect2 from GATK 4.1.1.0 and got an error:

A USER ERROR has occurred: standard-min-confidence-threshold-for-calling is not a recognized option

From the online documentation:

Note that the default was changed from 10.0 to 30.0 in version 4.1.0.0 to accompany the switch to use the the new quality score by default.

Thus, it was still maintained in 4.1.0.0. Based on that, I am surprised that it was removed.

There are actually a few other parameters that got dropped. For example, normal-artifact-lod from FilterMutectCalls. Are these changes explained somewhere?

[ldgauthier]

That argument is only relevant to HaplotypeCaller and GenotypeGVCFs. It should never have been available for Mutect2.

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On Thu, Mar 28, 2019, 11:09 PM igor ***@***.***> wrote: I just tried Mutect2 from GATK 4.1.1.0 and got an error: A USER ERROR has occurred: standard-min-confidence-threshold-for-calling is not a recognized option From the online documentation <https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.0.0/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php> : Note that the default was changed from 10.0 to 30.0 in version 4.1.0.0 to accompany the switch to use the the new quality score by default. Thus, it was still maintained in 4.1.0.0. Based on that, I am surprised that it was removed. I just wanted to confirm this was an intended change. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5845>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGRhdCF1GhJcFOFF4YvLqB_rB0x5oquxks5vbYQFgaJpZM4cRiVD> .

[davidbenjamin]

@igordot It used to exist because AssemblyBasedCallerArgumentCollection used to extend StandardCallerArgumentCollection, causing Mutect2 to have a bunch of HaplotypeCaller arguments that it didn't use. This was fixed in PR #5758.

FilterMutectCalls also lost a few arguments as part of a huge change to the entire filtering model in PR #5688. I'm working on a blog post about this but for now the Mutect2 docs at https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf are up-to-date and more user-friendly than they used to be.

[davidbenjamin]

If you get any more of these errors, it's either an argument that never had any effect or something that you 4.1.1 got rid of. In the latter case, you don't need to replace it with anything. In 4.1.1 FilterMutectCalls automatically learns a lot of parameters.