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(How to) Call somatic mutations using GATK4 Mutect2 #4745

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sooheelee opened this Issue May 7, 2018 · 4 comments

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sooheelee commented May 7, 2018

Question for @davidbenjamin and @takutosato.

do you have any documents for default parameters to run in tumor only mode? When I set af-of-alleles-not-in-resource = 0.001, I get no variants (GATK 4.0.0.0). When I set it to 0 (as recommended in this discussion: https://gatkforums.broadinstitute.org/gatk/discussion/10157/gatk4-beta-no-filter-passing-variants-in-mutect2-tumor-only-runs-using-default-parameters) I get over 3000 variants, so I am trying to find what is best way to determine this number for tumor only mode.


Hi @shlee,
If I am running Mutect2 with same samples but different parameters, do I really need to repeat the step 5 CollectSequencingArtifactMetrics? It looks like it's not dependent on the previous filtering step but as you emphasized this on the tutorial I wanted to check.
Another question is do you have any documents for default parameters to run in tumor only mode? When I set af-of-alleles-not-in-resource = 0.001, I get no variants (GATK 4.0.0.0). When I set it to 0 (as recommended in this discussion: https://gatkforums.broadinstitute.org/gatk/discussion/10157/gatk4-beta-no-filter-passing-variants-in-mutect2-tumor-only-runs-using-default-parameters) I get over 3000 variants, so I am trying to find what is best way to determine this number for tumor only mode.
Last but not least thanks a lot for this tutorial and documentation. I keep coming back and reading this as its loaded with information.
Best,
Irem

This Issue was generated from your [forums]
[forums]: https://gatkforums.broadinstitute.org/gatk/discussion/comment/48461#Comment_48461

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sooheelee commented May 7, 2018

Are we interested in writing some definitive guide on how to tune the af-of-alleles-not-in-resource parameter for different contexts?

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sooheelee commented May 7, 2018

@chandrans it appears that other researchers asked the same question. Apologies for not asking your involvement first.

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davidbenjamin commented May 8, 2018

@sooheelee In the latest release the tool automatically chooses different defaults for tumor-only versus tumor-normal, if no value is given. The best practice is now to specify nothing unless the user really knows what she is doing.

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sooheelee commented May 15, 2018

Thanks for following up with the researcher.

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