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CalculateGenotypePostiors minor updates to javadoc and logger type #5601

Merged
merged 2 commits into from
Jan 30, 2019
Merged

CalculateGenotypePostiors minor updates to javadoc and logger type #5601

merged 2 commits into from
Jan 30, 2019

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sooheelee
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  • Clarify tool documentation:
    • Update joint posteriors (JL) to joint posteriors (JP)
    • Remove statistical notes and provide link to GATK Article#11074 for background and math
    • Consolidate Notes and Caveats sections
    • Clarify at top the three different sources of priors and tool behavior regarding these
    • Clarify for family priors the tool only considers trio groups
    • Add Laura's comment that recent updates allow the tool to appropriately apply priors to indels
  • Change logger.info to logger.warn for situation where trio pedigree file is incomplete
    • Note that in this situation, in the absence of other refinement, the results are identical to the input

CalculateGenotypePostiors minor updates to javadoc and logger type
7117b05 
- Clarify tool documentation:
    - Remove statistical notes and provide link to GATK Article#11074 for background and math
    - Consolidate Notes and Caveats sections
    - Clarify at top the three different sources of priors and tool behavior regarding these
    - Clarify for family priors the tool only considers trio groups
    - Add Laura's comment that recent updates allow the tool to appropriately apply priors to indels
- Change logger.info to logger.warn for situation where trio pedigree file is incomplete
    - Note that in this situation, in the absence of other refinement, the results are identical to the input
@sooheelee sooheelee requested a review from ldgauthier January 23, 2019 21:34
@sooheelee sooheelee mentioned this pull request Jan 23, 2019
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@sooheelee
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Thank you at @ldgauthier for volunteering to review and for all of the feedback. The Travis checks are still in progress but the only code change is with the logger type.

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codecov-io commented Jan 23, 2019 •
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Codecov Report

Merging #5601 into master will decrease coverage by 0.026%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #5601       +/-   ##
===============================================
- Coverage     87.047%   87.021%   -0.026%     
- Complexity     31525     31624       +99     
===============================================
  Files           1928      1934        +6     
  Lines         145343    145816      +473     
  Branches       16090     16107       +17     
===============================================
+ Hits          126517    126891      +374     
- Misses         12966     13048       +82     
- Partials        5860      5877       +17
Impacted Files Coverage Δ Complexity Δ
...kers/variantutils/CalculateGenotypePosteriors.java 92.857% <100%> (ø) 17 <0> (ø) ⬇️
...walkers/genotyper/afcalc/AFCalculatorProvider.java 22.222% <0%> (-44.444%) 2% <0%> (-2%)
...notyper/afcalc/ConcurrentAFCalculatorProvider.java 50% <0%> (-33.333%) 1% <0%> (-1%)
...nder/utils/downsampling/PositionalDownsampler.java 88.462% <0%> (-11.538%) 22% <0%> (+1%)
...er/engine/spark/datasources/VariantsSparkSink.java 78.125% <0%> (-11.53%) 8% <0%> (-1%)
...broadinstitute/hellbender/engine/FeatureInput.java 88.235% <0%> (-4.82%) 19% <0%> (+1%)
...r/tools/walkers/mutect/Mutect2FilteringEngine.java 80.743% <0%> (-4.581%) 89% <0%> (ø)
...rs/genotyper/afcalc/FixedAFCalculatorProvider.java 88.889% <0%> (-3.704%) 12% <0%> (ø)
...ute/hellbender/utils/test/FuncotatorTestUtils.java 95.161% <0%> (-3.084%) 7% <0%> (+1%)
...GATKPlugin/GATKReadFilterPluginDescriptorTest.java 88.62% <0%> (-1.76%) 48% <0%> (+1%)
... and 64 more

@sooheelee
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Testing with the branch gives the expected WARN.

10:36:48.710 WARN  CalculateGenotypePosteriors - No PED file passed or no *non-skipped* trios found in PED file. Skipping family priors.

The WARN is in the middle of the INFO fields and not separate at the bottom of the stdout:
screenshot 2019-01-24 10 37 19

ldgauthier
ldgauthier requested changes Jan 24, 2019
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Some clarifications.

...va/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors.java Show resolved Hide resolved
...va/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors.java Outdated
* independently. This assumption of independent draws follows from the assumption of Hardy-Weinberg equilibrium (HWE).
* Thus, HWE is imposed on the likelihoods as a result of CalculateGenotypePosteriors.</p>
* <p>
* The tool uses priors from three different data sources: (i) one or more supporting germline population callsets
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Can we say something more like "The tool can use priors from three different data sources"? Most cases won't use all three.

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What are the annotations, specifically?

The tool will use MLEAC if available or AC if MLEAC is not provided. AN is also required unless genotypes are provided for all samples.

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@ldgauthier, the tool document already covers the MLEAC/AC annotations in the bullet point on L51.

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Changing 'The tool uses priors from' to 'The tool can use priors from'. Will add in the specific annotations exactly as you word it in a section below as it is much clearer than the current bullet point.

...va/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors.java Show resolved Hide resolved
...va/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors.java Outdated
*
* <h3>Inputs</h3>
* <p>
* <ul>
* <li>A VCF with genotype likelihoods, and optionally genotypes, AC/AN fields, or MLEAC/AN fields.</li>
* <li>(Optional) A PED pedigree file containing the description of the relationships between individuals.</li>
* <li>(Optional) A PED pedigree file containing the description of the relationships between individuals. Only
* trio groups are considered in the calculations.</li>
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Should we be absolutely specific that we mean mother-father-offspring trios?

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What is meant by trios is I think clear. However, I see now we do not mention this anywhere and so I will add this.

...va/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors.java Outdated
@@ -80,6 +86,17 @@
* For any non-SNP sites in the input callset, flat priors are applied.
* </p>
*
* <p>
* For the latest versions of the tool in which this message appears, the tool appropriately applies priors to indels.
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as of 4.0.5.0

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Added. Thank you.

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Back to you @sooheelee

Second round of updates that incorporate feedback from Laura
2415676 
- Add tool order of ingestion of annotations MLEAC vs AC and detail on AN requirement
- Specifically define that trios are mother-father-offspring
- Add version that appropriately applies priors to indels (4.0.5.0)
- Smooth writing
@sooheelee
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I've incorporated your feedback @ldgauthier.

ldgauthier
ldgauthier approved these changes Jan 30, 2019
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👍 Sorry I missed this in the flurry of github emails yesterday.

@sooheelee sooheelee merged commit 78df6b2 into master Jan 30, 2019
@sooheelee sooheelee deleted the shlee_cgp branch January 30, 2019 22:44
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No worries Laura. Thanks again for the feedback.

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@sooheelee @codecov-io @ldgauthier @davidbenjamin