VS-1657 - Adding new annotations to the sites-only VCF. #9212
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Pull Request Overview
This PR adds new annotations to the sites-only VCF to support additional variant features. Key changes include:
- Adding new attributes in ExtractFeaturesEngine.java for strand bias, allele-specific variant depth, and mapping-quality combined with depth.
- Updating header definitions in ExtractFeatures.java for the new annotation keys.
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeaturesEngine.java | Adds new attribute calculations and annotation assignments for strand bias and depth metrics |
| src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeatures.java | Updates VCF header definitions to include the newly added annotation keys |
| import org.broadinstitute.hellbender.tools.walkers.annotator.QualByDepth; | ||
| import org.broadinstitute.hellbender.tools.walkers.annotator.StrandOddsRatio; | ||
| import org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine; | ||
| import org.broadinstitute.hellbender.tools.walkers.annotator.*; |
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Consider replacing the wildcard import with explicit class imports to improve code clarity and prevent potential namespace pollution.
Suggested change
| import org.broadinstitute.hellbender.tools.walkers.annotator.*; | |
| import org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet; | |
| import org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine; |
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| final List<Integer> sbValues = Arrays.asList(sb_ref_plus, sb_ref_minus, sb_alt_plus, sb_alt_minus); | ||
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| // Create the AS_SB_TABLE annotation - allele-specific strand bias information | ||
| final String asSbTable = String.format("%d,%d|%d,%d", sb_ref_plus, sb_ref_minus, sb_alt_plus, sb_alt_minus); | ||
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| // Calculate the simple SB (Strand Bias) value | ||
| // This is typically a Phred-scaled value - we'll use the Fisher's Exact Test p-value | ||
| double sbValue = QualityUtils.phredScaleErrorRate(FisherStrand.pValueForContingencyTable(refAltTable)); | ||
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| double fs = QualityUtils.phredScaleErrorRate(Math.max(FisherStrand.pValueForContingencyTable(refAltTable), AS_StrandBiasTest.MIN_PVALUE)); | ||
| double sor = StrandOddsRatio.calculateSOR(refAltTable); |
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[nitpick] Consider encapsulating the annotation attribute assignments (lines 285-331) into dedicated helper methods to reduce duplication and improve readability.
Suggested change
| final List<Integer> sbValues = Arrays.asList(sb_ref_plus, sb_ref_minus, sb_alt_plus, sb_alt_minus); | |
| // Create the AS_SB_TABLE annotation - allele-specific strand bias information | |
| final String asSbTable = String.format("%d,%d|%d,%d", sb_ref_plus, sb_ref_minus, sb_alt_plus, sb_alt_minus); | |
| // Calculate the simple SB (Strand Bias) value | |
| // This is typically a Phred-scaled value - we'll use the Fisher's Exact Test p-value | |
| double sbValue = QualityUtils.phredScaleErrorRate(FisherStrand.pValueForContingencyTable(refAltTable)); | |
| double fs = QualityUtils.phredScaleErrorRate(Math.max(FisherStrand.pValueForContingencyTable(refAltTable), AS_StrandBiasTest.MIN_PVALUE)); | |
| double sor = StrandOddsRatio.calculateSOR(refAltTable); | |
| final List<Integer> sbValues = createSBTable(sb_ref_plus, sb_ref_minus, sb_alt_plus, sb_alt_minus); | |
| // Create the AS_SB_TABLE annotation - allele-specific strand bias information | |
| final String asSbTable = createASSBTable(sb_ref_plus, sb_ref_minus, sb_alt_plus, sb_alt_minus); | |
| // Calculate the simple SB (Strand Bias) value | |
| double sbValue = calculateSBValue(refAltTable); | |
| // Calculate FS and SOR values | |
| double fs = calculateFSValue(refAltTable); | |
| double sor = calculateSORValue(refAltTable); |
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This PR adds annotations to the sites-only VCF as requested by Conrad
Integration test here