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Added a '--prefer-mane-transcripts' mode that enforces MANE_Select tagged Gencode transcripts where possible #9012

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merged 3 commits into from
Oct 23, 2024
Merged

Added a '--prefer-mane-transcripts' mode that enforces MANE_Select tagged Gencode transcripts where possible #9012

merged 3 commits into from
Oct 23, 2024

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jamesemery
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@jamesemery jamesemery requested a review from jonn-smith October 18, 2024 19:34
@jamesemery jamesemery mentioned this pull request Oct 18, 2024
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jonn-smith
jonn-smith requested changes Oct 22, 2024
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Looks pretty good. Some requests for more tests.

Also, can you describe what you changed and / or added to the git LFS / large files?

...in/java/org/broadinstitute/hellbender/tools/funcotator/BaseFuncotatorArgumentCollection.java Outdated Show resolved Hide resolved
...roadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/DataSourceUtils.java Outdated Show resolved Hide resolved
...roadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java Outdated Show resolved Hide resolved
...roadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java Outdated
@@ -863,6 +892,11 @@ private List<GencodeFuncotation> createFuncotationsHelper(final VariantContext v
transcriptList = gtfFeature.getTranscripts();
}

// Filter out the non-MANE_Select/Mane_Plus_Clinical transcripts if we're only using MANE transcripts:
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Can you rename the input variable in the following method to reflect that the transcripts no longer need to be only basic?

private List<GencodeFuncotation> createFuncotationsHelper(final VariantContext variant, final Allele altAllele, final ReferenceContext reference, final List<GencodeGtfTranscriptFeature> basicTranscripts)

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that is not accurate though, the transcripts still have to be basic. This simply applies a layer on-top of the basic transcript filtering that enforces that they are MANE select as well (which my cursory survey of gtf files seemed to indicated travels together anyway)

src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java Show resolved Hide resolved
...roadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java Outdated Show resolved Hide resolved
src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java Show resolved Hide resolved
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@jonn-smith i added a readme in the LFS files. Looks like github won't display it though which is slightly annoying. Here is what it says (WARNING.txt: NOTE: this gencode.v43.PIK3CA.gtf file is slightly edited for the sake of testing MANE_SELECT and MANE_PLUS_CLINICAL.
transcript "ENST00000643187.1" is not actually classified as MANE_Plus_Clinical but it is included in the file for testing purposes.)

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jonn-smith requested changes Oct 22, 2024
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A few more quick changes requested.

Also, can you rename any of the resource files checked into the large files repo that you modified to have descriptive names? Something like "MANE_PLUS_CLINICAL_test_data.gtf" would be fine.

...itute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java Outdated Show resolved Hide resolved
...itute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java Outdated Show resolved Hide resolved
src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java Outdated Show resolved Hide resolved
jonn-smith
jonn-smith approved these changes Oct 22, 2024
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Looks good.

👍

@jonn-smith jonn-smith merged commit c4860d4 into master Oct 23, 2024
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@jonn-smith jonn-smith deleted the je_ManeTranscriptModeFunctotator branch October 23, 2024 12:49
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