zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

De Novo SNP caller as presented at 1KG meeting on 9/10/09 with min LOD 5 calls required from both parents and a LOD 5 call in the daugter gold standard concordant call set. All SNP calls must be present as bound RODs. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1590 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-09-11 19:30:23 +00:00
parent 0f3049652a
commit 5354c1876c
1 changed files with 67 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

67
java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java 100755
View File

@ -0,0 +1,67 @@
package org.broadinstitute.sting.playground.gatk.walkers;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.GenotypeUtils;
import java.util.List;
import java.util.Collection;
/**
* Created by IntelliJ IDEA.
* User: andrewk
* Date: Sep 1, 2009
* Time: 11:04:55 AM
* To change this template use File | Settings | File Templates.
*/
@By(DataSource.REFERENCE)
@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="child",type= AllelicVariant.class), @RMD(name="parent1",type= AllelicVariant.class), @RMD(name="parent2",type= AllelicVariant.class)})
//@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=AllelicVariant.class), @RMD(name="dbsnp",type=AllelicVariant.class),@RMD(name="hapmap-chip",type=AllelicVariant.class), @RMD(name="interval",type=IntervalRod.class)})
//@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="dbsnp",type=AllelicVariant.class)})
public class DeNovoSNPWalker extends RefWalker<String, Integer>{
public String map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
AllelicVariant child = (AllelicVariant)tracker.lookup("child", null);
AllelicVariant parent1 = (AllelicVariant)tracker.lookup("parent1", null);
AllelicVariant parent2 = (AllelicVariant)tracker.lookup("parent2", null);
AllelicVariant dbsnp = (AllelicVariant)tracker.lookup("dbSNP", null);
if (child != null && parent1 != null && parent2 != null) {
if (child.isSNP() &&
child.getVariationConfidence() > 5 && // BTR > 5
parent1.isReference() &&
parent1.getConsensusConfidence() > 5 &&
parent2.isReference() &&
parent2.getConsensusConfidence() > 5
) {
double sumConfidences = 0.5 * (0.5 * child.getVariationConfidence() + Math.min(parent1.getConsensusConfidence(), parent2.getConsensusConfidence()));
out.format("%s\t", child.getLocation().getContig());
out.format("%s\t", child.getLocation().getStart());
out.format("%.4f\t", sumConfidences);
out.format("%.4f\t", child.getVariationConfidence());
out.format("%.4f\t", parent1.getConsensusConfidence());
out.format("%.4f\t", parent2.getConsensusConfidence());
out.format("%s\t", dbsnp != null);
out.format ("%s\t", child.toString());
out.format ("%s\t", parent1.toString());
out.format ("%s", parent2.toSimpleString());
if (dbsnp != null)
out.format ("\tDBSNP\t:%s", dbsnp.toString());
out.println();
}
}
return "";
}
public Integer reduceInit() { return 0; }
public Integer reduce(String line, Integer a) {
return 1;
}
}