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Added ValidationData analysis type to VariantEvalWalker; this eval takes a GFF file with validated truth data positions (bound to "validation")and calculates the accuracy of the genotype calls bound to "eval". 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1862 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-10-16 15:39:08 +00:00
parent 07b134a124
commit d1a4cd2f73
3 changed files with 59 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -444,7 +444,7 @@ public class GenomeAnalysisEngine {
// Check to see that no forbidden rods are present.
for (ReferenceOrderedData<? extends ReferenceOrderedDatum> rod : rods) {
if (!WalkerManager.isAllowed(walker, rod))
throw new ArgumentException(String.format("Walker does not allow access to metadata: %s. If this is incorrect, change the @Allows metadata", rod.getName()));
throw new ArgumentException(String.format("Walker of type %s does not allow access to metadata: %s. If this is incorrect, change the @Allows metadata", walker.getClass(), rod.getName()));
}
}

56
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ValidationDataAnalysis.java 100755
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@ -0,0 +1,56 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import java.util.List;
import java.util.ArrayList;
/**
* Created by IntelliJ IDEA.
* User: andrewk
* Date: Sep 30, 2009
* Time: 5:28:57 PM
* To change this template use File | Settings | File Templates.
*/
// @Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=VariationRod.class), @RMD(name="dbsnp",type= rodDbSNP.class),@RMD(name="hapmap-chip",type=RodGenotypeChipAsGFF.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)})
public class ValidationDataAnalysis extends BasicVariantAnalysis implements GenotypeAnalysis, PopulationAnalysis {
private int calls_at_validated_sites = 0;
private int calls_at_sites_validated_true = 0;
private int validated_sites = 0;
public ValidationDataAnalysis() {
super("validation_data_analysis");
}
public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
validated_sites++;
Variation val_data = (Variation) tracker.lookup("validation", null);
Variation dbsnp = (Variation) tracker.lookup("dbsnp",null);
if (eval != null) {
calls_at_sites_validated_true++;
//out.format("Has validaiton data: %s\n", val_data.getLocation());
if (val_data != null) {
//out.format("Validated true: %s\n", val_data.getLocation());
calls_at_validated_sites++;
}
}
out.println(context.getLocation());
return "";
}
public List<String> done() {
List<String> s = new ArrayList<String>();
s.add(String.format("validated sites %d", validated_sites));
s.add(String.format("calls at validated sites %d", calls_at_sites_validated_true));
s.add(String.format("calls at sites validated true %d", calls_at_validated_sites));
s.add(String.format("%% validated true %f", (float) calls_at_validated_sites / calls_at_sites_validated_true));
return s;
}
}

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -26,7 +26,7 @@ import java.util.*;
*
*/
@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=ReferenceOrderedDatum.class)}) // right now we have no base variant class for rods, this should change
@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=ReferenceOrderedDatum.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=ReferenceOrderedDatum.class), @RMD(name="interval",type=IntervalRod.class)})
@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=ReferenceOrderedDatum.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=ReferenceOrderedDatum.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)})
public class VariantEvalWalker extends RefWalker<Integer, Integer> {
@Argument(shortName="minConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
public int minConfidenceScore = -1;
@ -115,6 +115,7 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
//
// Add new analyses here!
//
analyses.add(new ValidationDataAnalysis());
analyses.add(new PooledGenotypeConcordance(pathToHapmapPoolFile));
analyses.add(new VariantCounter());
analyses.add(new VariantDBCoverage(knownSNPDBName));