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Moved MQ0 out of HC exclusion and into StandardUGAnnotation

This commit is contained in:
Geraldine Van der Auwera 2015-05-03 01:04:49 +02:00
parent 071d82d1bf
commit 5d8b9a7c20
3 changed files with 12 additions and 8 deletions
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6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java
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@ -57,7 +57,7 @@ import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardUGAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
@ -79,7 +79,7 @@ import java.util.Map;
* <p>This anotation gives you the count of all reads that have MAPQ = 0 across all samples. The count of reads with MAPQ0 can be used for quality control; high counts typically indicate regions where it is difficult to make confident calls.</p>
*
* <h3>Caveat</h3>
* <p>This annotation is excluded by HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation would always return a value of 0 anyway.</p>
* <p>It is not useful to apply this annotation with HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation will always return a value of 0.</p>
*
* <h3>Related annotations</h3>
* <ul>
@ -88,7 +88,7 @@ import java.util.Map;
* </ul>
*
*/
public class MappingQualityZero extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
public class MappingQualityZero extends InfoFieldAnnotation implements StandardUGAnnotation, ActiveRegionBasedAnnotation {
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,

12
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -293,12 +293,16 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
protected List<String> annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"ClippingRankSumTest", "DepthPerSampleHC"}));
/**
* Which annotations to exclude from output in the VCF file. Note that this argument has higher priority than the -A or -G arguments,
* so these annotations will be excluded even if they are explicitly included with the other options.
* Which annotations to exclude from output in the VCF file. Note that this argument has higher priority than the
* -A or -G arguments, so these annotations will be excluded even if they are explicitly included with the other
* options. When HaplotypeCaller is run with -ERC GVCF or -ERC BP_RESOLUTION, some annotations are excluded from the
* output by default because they will only be meaningful once they have been recalculated by GenotypeGVCFs. As
* of version 3.3 this concerns ChromosomeCounts, FisherStrand, StrandOddsRatio and QualByDepth.
*
*/
@Advanced
@Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false)
protected List<String> annotationsToExclude = new ArrayList<>(Arrays.asList(new String[]{"MappingQualityZero", "MappingQualityZeroBySample"}));
protected List<String> annotationsToExclude = new ArrayList<>(Arrays.asList(new String[]{}));
/**
* Which groups of annotations to add to the output VCF file. The single value 'none' removes the default group. See
@ -506,7 +510,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
}
if (dontGenotype && emitReferenceConfidence())
throw new UserException("You cannot request gVCF output and do not genotype at the same time");
throw new UserException("You cannot request gVCF output and 'do not genotype' at the same time");
if ( emitReferenceConfidence() ) {

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java
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@ -50,7 +50,7 @@ import java.util.List;
* <p>This annotation gives you the count of all reads that have MAPQ = 0 for each sample. The count of reads with MAPQ0 can be used for quality control; high counts typically indicate regions where it is difficult to make confident calls.</p>
*
* <h3>Caveat</h3>
* <p>This annotation is excluded by HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation would always return a value of 0 anyway.</p>
* <p>It is not useful to apply this annotation with HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation will always return a value of 0.</p>
*
* <h3>Related annotations</h3>
* <ul>