Reword comments in Mutect2.wdl #5196
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@LeeTL1220 please review |
scripts/mutect2_wdl/mutect2.wdl
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| ## run_orientation_bias_filter: (deprecated) if true, run the orientation bias filter (optional) | ||
| ## run_orientation_bias_mixture_model_filter: if true, filter orientation bias sites based on the posterior probabilities computed by the read orientation artifact mixture model (optional) | ||
| ## run_orientation_bias_filter: if true, run the orientation bias filter (optional) | ||
| ## run_orientation_bias_mixture_model_filter: if true, filter orientation bias sites with the read orientation artifact mixture model, which is the recommended orientation bias filter (optional) |
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Do you want to add a comment about NovaSeq?
Can you add a comment that artifact modes parameter is ignored, since these are automatically detected in the mixture model filter?
Can you add a reference to D-ToxoG for the old filter? https://software.broadinstitute.org/cancer/cga/dtoxog
"This filter is a GATK implementation of D-ToxoG (url) with modifications to allow multiple artifact modes."
Also, we should discuss whether we want to flip the default in FireCloud to be the new filter. Since we are recommending it.
Also, I want to confirm that you have slides with results for the no-artifact case? I.e. that there is no filtering when there is no orientation bias. I want to make sure we have formal results to present before we say it is recommended.
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Can you run both filters at the same time? If not, can you add a comment to that effect?
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All done. The evaluation results are in the palantir repo: https://github.com/broadinstitute/palantir/pull/671
scripts/mutect2_wdl/mutect2.wdl
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| @@ -796,6 +796,7 @@ task CollectF1R2Counts { | |||
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| # Learning step of the orientation bias mixture model, which is the recommended orientation bias filter as of September 2017 | |||
scripts/mutect2_wdl/mutect2.wdl
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| @@ -737,6 +736,7 @@ task CollectSequencingArtifactMetrics { | |||
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| # Data collection step of the orientation bias mixture model, which is the recommended orientation bias filter as of September 2017 | |||
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@takutosato @droazen Can we make sure that this gets in the next release? Users may misinterpret the deprecation warning that is removed in this PR. |
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@LeeTL1220 thanks for your comments. Yes, I will make suggested changes by the end of the week, if not later today |
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@LeeTL1220 back to you |
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@takutosato back to you. |
Codecov Report
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## master #5196 +/- ##
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+ Coverage 86.791% 86.798% +0.007%
+ Complexity 29723 29711 -12
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Files 1820 1820
Lines 137462 137406 -56
Branches 15171 15160 -11
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- Hits 119304 119265 -39
+ Misses 12649 12637 -12
+ Partials 5509 5504 -5
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@davidbenjamin @takutosato I approved this and it needs to be in the next release. What is holding up a merge? |
In particular, do not call the old orientation bias filter deprecated