Now, if a dbsnp rod is passed to either the UnifiedGenotyper or VariantAnnotator, a DB=0/1 annotation is added (in addition to filling in the ID field); this is in line with 1KG project calls. If no dbsnp rod is used, the annotation is not added (as opposed to setting every entry to DB=0).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2678 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 import org.broadinstitute.sting.gatk.contexts.*;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 import org.broadinstitute.sting.utils.genotype.*;
@@ -41,6 +42,9 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
 
     private ArrayList<VariantAnnotation> requestedAnnotations;
 
+    // should we annotate dbsnp?
+    private boolean annotateDbsnp = false;
+
     // mapping from class name to class
     private static HashMap<String, VariantAnnotation> allAnnotations = null;
     private static HashMap<String, VariantAnnotation> standardAnnotations = null;
@@ -115,12 +119,24 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
             }
         }
 
+        // check to see whether a dbsnp rod was included
+        List<ReferenceOrderedDataSource> dataSources = getToolkit().getRodDataSources();
+        for ( ReferenceOrderedDataSource source : dataSources ) {
+            ReferenceOrderedData rod = source.getReferenceOrderedData();
+            if ( rod.getType().equals(rodDbSNP.class) ) {
+                annotateDbsnp = true;
+                break;
+            }
+        }
+
         // setup the header fields
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
         hInfo.add(new VCFHeaderLine("source", "VariantAnnotator"));
         hInfo.add(new VCFHeaderLine("annotatorReference", getToolkit().getArguments().referenceFile.getName()));
         hInfo.addAll(getVCFAnnotationDescriptions(requestedAnnotations));
+        if ( annotateDbsnp )
+            hInfo.add(new VCFInfoHeaderLine(VCFRecord.DBSNP_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "dbSNP membership"));
 
         vcfWriter = new VCFWriter(VCF_OUT);
         vcfHeader = new VCFHeader(hInfo, samples);
@@ -166,7 +182,7 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
         if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) {
             Map<String, StratifiedAlignmentContext> stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup());
             if ( stratifiedContexts != null )
-                annotations = getAnnotations(tracker, ref, stratifiedContexts, variant, requestedAnnotations);
+                annotations = getAnnotations(tracker, ref, stratifiedContexts, variant, requestedAnnotations, annotateDbsnp);
         }
         writeVCF(tracker, ref, context, variant, annotations);
 
@@ -208,24 +224,30 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
     }
 
     // option #1: don't specify annotations to be used: standard annotations are used by default
-    public static Map<String, String> getAnnotations(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
+    public static Map<String, String> getAnnotations(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation, boolean annotateDbsnp) {
         if ( standardAnnotations == null )
             determineAllAnnotations();
-        return getAnnotations(tracker, ref, stratifiedContexts, variation, standardAnnotations.values());
+        return getAnnotations(tracker, ref, stratifiedContexts, variation, standardAnnotations.values(), annotateDbsnp);
     }
 
     // option #2: specify that all possible annotations be used
-    public static Map<String, String> getAllAnnotations(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
+    public static Map<String, String> getAllAnnotations(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation, boolean annotateDbsnp) {
         if ( allAnnotations == null )
             determineAllAnnotations();
-        return getAnnotations(tracker, ref, stratifiedContexts, variation, allAnnotations.values());
+        return getAnnotations(tracker, ref, stratifiedContexts, variation, allAnnotations.values(), annotateDbsnp);
     }
 
     // option #3: specify the exact annotations to be used
-    public static Map<String, String> getAnnotations(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation, Collection<VariantAnnotation> annotations) {
+    public static Map<String, String> getAnnotations(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation, Collection<VariantAnnotation> annotations, boolean annotateDbsnp) {
 
         HashMap<String, String> results = new HashMap<String, String>();
 
+        // annotate dbsnp occurrence
+        if ( annotateDbsnp ) {
+            rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getTrackData("dbsnp", null));
+            results.put(VCFRecord.DBSNP_KEY, dbsnp == null ? "0" : "1");
+        }
+
         for ( VariantAnnotation annotator : annotations) {
             String annot = annotator.annotate(tracker, ref, stratifiedContexts, variation);
             if ( annot != null ) {
@@ -236,13 +258,12 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
         return results;
     }
 
-
     private void writeVCF(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariationRod variant, Map<String, String> annotations) {
         VCFRecord rec = getVCFRecord(tracker, ref, context, variant);
         if ( rec != null ) {
             rec.addInfoFields(annotations);
             // also, annotate dbsnp id if available and not already there
-            if ( rec.getID() == null || rec.getID().equals(".") ) {
+            if ( annotateDbsnp && (rec.getID() == null || rec.getID().equals(".")) ) {
                 rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getTrackData("dbsnp", null));
                 if ( dbsnp != null )
                     rec.setID(dbsnp.getRS_ID());

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -26,8 +26,11 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.contexts.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
+import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator;
 import org.broadinstitute.sting.utils.*;
@@ -66,7 +69,10 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     // samples in input
     private Set<String> samples = new HashSet<String>();
 
-    /** Enable deletions in the pileup **/
+    // should we annotate dbsnp?
+    private boolean annotateDbsnp = false;
+
+    // Enable deletions in the pileup
     public boolean includeReadsWithDeletionAtLoci() { return true; }
 
     /**
@@ -162,6 +168,16 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
             beagleWriter.println();
         }
 
+        // check to see whether a dbsnp rod was included
+        List<ReferenceOrderedDataSource> dataSources = getToolkit().getRodDataSources();
+        for ( ReferenceOrderedDataSource source : dataSources ) {
+            ReferenceOrderedData rod = source.getReferenceOrderedData();
+            if ( rod.getType().equals(rodDbSNP.class) ) {
+                annotateDbsnp = true;
+                break;
+            }
+        }
+
         // *** If we were called by another walker, then we don't ***
         // *** want to do any of the other initialization steps.  ***
         if ( writer == null )
@@ -192,6 +208,8 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
 
         // annotation (INFO) fields from UnifiedGenotyper
         headerInfo.add(new VCFInfoHeaderLine(VCFRecord.ALLELE_FREQUENCY_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Allele Frequency"));
+        if ( annotateDbsnp )
+            headerInfo.add(new VCFInfoHeaderLine(VCFRecord.DBSNP_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "dbSNP membership"));
         if ( !UAC.NO_SLOD )
             headerInfo.add(new VCFInfoHeaderLine(VCFRecord.STRAND_BIAS_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Strand Bias"));
 
@@ -274,9 +292,9 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
 
             Map<String, String> annotations;
             if ( UAC.ALL_ANNOTATIONS )
-                annotations = VariantAnnotator.getAllAnnotations(tracker, refContext, stratifiedContexts, call.variation);
+                annotations = VariantAnnotator.getAllAnnotations(tracker, refContext, stratifiedContexts, call.variation, annotateDbsnp);
             else
-                annotations = VariantAnnotator.getAnnotations(tracker, refContext, stratifiedContexts, call.variation);
+                annotations = VariantAnnotator.getAnnotations(tracker, refContext, stratifiedContexts, call.variation, annotateDbsnp);
             ((ArbitraryFieldsBacked)call.variation).setFields(annotations);
         }