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Fix overfiltering in M2 in GGA alleles with no reads #5743

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Mar 3, 2019
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Fix overfiltering in M2 in GGA alleles with no reads #5743

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390a7c0
fix a bug where GGA allele with no reads leads to mapping quality fil…
davidbenjamin Mar 1, 2019
6323853
likewise for read position filter
davidbenjamin Mar 1, 2019
9ee85fc
test
davidbenjamin Mar 3, 2019
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5 changes: 4 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQuality.java
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Expand Up @@ -20,9 +20,12 @@
@DocumentedFeature(groupName=HelpConstants.DOC_CAT_ANNOTATORS, groupSummary=HelpConstants.DOC_CAT_ANNOTATORS_SUMMARY, summary="Median mapping quality of reads supporting each allele (MMQ)")
public class MappingQuality extends PerAlleleAnnotation implements StandardMutectAnnotation {

// we don't want a GGA mode allele with no reads to prejudice us against a site so we assign a good mapping quality
private static final int VALUE_FOR_NO_READS = 60;

@Override
protected int aggregate(final List<Integer> values) {
return values.isEmpty() ? 0 : MathUtils.median(Ints.toArray(values));
return values.isEmpty() ? VALUE_FOR_NO_READS : MathUtils.median(Ints.toArray(values));
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Are you sure you want to do this for all runs of M2, not just the GGA runs?

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Just seems like there could be a downstream effect.

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Yes, because any allele with no reads should have no say either way. But also, an allele with no reads can't occur outside of GGA mode.

}

@Override
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5 changes: 4 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosition.java
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Expand Up @@ -34,9 +34,12 @@
@DocumentedFeature(groupName=HelpConstants.DOC_CAT_ANNOTATORS, groupSummary=HelpConstants.DOC_CAT_ANNOTATORS_SUMMARY, summary="Median distance of variant starts from ends of reads supporting each allele (MPOS)")
public class ReadPosition extends PerAlleleAnnotation implements StandardMutectAnnotation {

// we don't want a GGA mode allele with no reads to prejudice us against a site so we assign a non-suspicious value
private static final int VALUE_FOR_NO_READS = 50;

@Override
protected int aggregate(final List<Integer> values) {
return values.isEmpty() ? 0 : MathUtils.median(Ints.toArray(values));
return values.isEmpty() ? VALUE_FOR_NO_READS : MathUtils.median(Ints.toArray(values));
}

@Override
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