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Gc getpipeupsummaries use mappingqualityreadfilter #8781

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merged 3 commits into from
Apr 18, 2024
Merged

Gc getpipeupsummaries use mappingqualityreadfilter #8781

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d2af3f5
Add MappingQualityReadFilter
gokalpcelik Apr 17, 2024
a9300a6
Added additional warnings for mmq
gokalpcelik Apr 17, 2024
0436ef7
Fixed doc typo
gokalpcelik Apr 18, 2024
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18 changes: 11 additions & 7 deletions ...in/java/org/broadinstitute/hellbender/tools/walkers/contamination/GetPileupSummaries.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.cmdline.programgroups.CoverageAnalysisProgramGroup;
import org.broadinstitute.hellbender.engine.*;
import org.broadinstitute.hellbender.engine.filters.MappingQualityReadFilter;
import org.broadinstitute.hellbender.engine.filters.ReadFilter;
import org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary;
import org.broadinstitute.hellbender.engine.filters.WellformedReadFilter;
Expand Down Expand Up @@ -100,6 +101,13 @@
* file that have AF of 0.01 or more.
* </p>
*
* <p>
* Finally for those using mappers other than bwa mem or dragen-os, {@code --minimum-mapping-quality} threshold is
* set to 50, which limits the usable reads that tool considers for generating pileups. Certain mappers are known to
* assign scores less that this threshold even for the unique mappers. If you observe all empty results in your
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Did you mean "unique mappings" rather than "unique mappers"?

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Ah yes. Typo at midnight. I will fix it shortly.

* summary file please adjust the {@code --minimum-mapping-quality} parameter according to your input files.
* </p>
*
*/
@CommandLineProgramProperties(
summary = "Tabulates pileup metrics for inferring contamination",
Expand All @@ -112,8 +120,7 @@ public class GetPileupSummaries extends LocusWalker {
public static final String MIN_SITE_AF_LONG_NAME = "minimum-population-allele-frequency";
public static final String MAX_SITE_AF_SHORT_NAME = "max-af";
public static final String MIN_SITE_AF_SHORT_NAME = "min-af";
public static final String MIN_MAPPING_QUALITY_LONG_NAME = "min-mapping-quality";
public static final String MIN_MAPPING_QUALITY_SHORT_NAME = "mmq";


private static final double DEFAULT_MIN_POPULATION_AF = 0.01;
private static final double DEFAULT_MAX_POPULATION_AF = 0.2;
Expand All @@ -137,9 +144,6 @@ public class GetPileupSummaries extends LocusWalker {
doc = "Maximum population allele frequency of sites to consider.", optional = true)
private double maxPopulationAlleleFrequency = DEFAULT_MAX_POPULATION_AF;

@Argument(fullName = MIN_MAPPING_QUALITY_LONG_NAME, shortName = MIN_MAPPING_QUALITY_SHORT_NAME, doc = "Minimum read mapping quality", optional = true)
private int minMappingQuality = DEFAULT_MINIMUM_MAPPING_QUALITY;

private boolean sawVariantsWithoutAlleleFrequency = false;
private boolean sawVariantsWithAlleleFrequency = false;

Expand Down Expand Up @@ -168,6 +172,7 @@ public boolean requiresFeatures() {
@Override
public List<ReadFilter> getDefaultReadFilters() {
final List<ReadFilter> filters = new ArrayList<>();
filters.add(new MappingQualityReadFilter(DEFAULT_MINIMUM_MAPPING_QUALITY));
filters.add(ReadFilterLibrary.MAPPING_QUALITY_AVAILABLE);
filters.add(ReadFilterLibrary.MAPPING_QUALITY_NOT_ZERO);
filters.add(ReadFilterLibrary.MAPPED);
Expand Down Expand Up @@ -208,8 +213,7 @@ public void apply(AlignmentContext alignmentContext, ReferenceContext referenceC
final VariantContext vc = vcs.get(0);

if ( vc.isBiallelic() && vc.isSNP() && alleleFrequencyInRange(vc) ) {
final ReadPileup pileup = alignmentContext.getBasePileup()
.makeFilteredPileup(pe -> pe.getRead().getMappingQuality() >= minMappingQuality);
final ReadPileup pileup = alignmentContext.getBasePileup();
try {
writer.writeRecord(new PileupSummary(vc, pileup));
} catch (final IOException ex) {
Expand Down
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