From fa7284b7a11e148790620671c508dc2539998c55 Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 8 Mar 2011 22:10:38 +0000
Subject: [PATCH] Genotype And Validate walker is now ready to be used by
 anyone.

given an annotated VCF and a BAM file, it genotypes (using the reads in the BAM) each variant in the VCF (for snp or indel) and validates (or not) the 'known' annotation. Outputs a truth table with the PPV and NPV values, and optionally a vcf file with the variants that had enough coverage to be validated. You can optionally provide a minimum depth of coverage and only do the analysis conditional on that. (will write a wiki for this walker, as it might be useful for future validation essays).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5409 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/GenotypeAndValidateWalker.java    | 51 ++++++++++++++-----
 1 file changed, 37 insertions(+), 14 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/GenotypeAndValidateWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/GenotypeAndValidateWalker.java
index 125166e0d..16afd8912 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/GenotypeAndValidateWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/GenotypeAndValidateWalker.java
@@ -25,11 +25,16 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
+import com.google.common.collect.ImmutableSet;
 import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broad.tribble.vcf.VCFHeader;
+import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
@@ -39,8 +44,8 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
-import java.io.PrintStream;
 import java.util.*;
 
 /**
@@ -61,15 +66,18 @@ import java.util.*;
 
 public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalker.CountedData, GenotypeAndValidateWalker.CountedData> {
 
+    @Output(doc="File to which validated variants should be written", required=true)
+    protected VCFWriter vcfWriter = null;
+
     @Argument(fullName="minimum_base_quality_score", shortName="mbq", doc="Minimum base quality score for calling a genotype", required=false)
     private int mbq = -1;
 
     @Argument(fullName="maximum_deletion_fraction", shortName="deletions", doc="Maximum deletion fraction for calling a genotype", required=false)
     private double deletions = -1;
 
+    @Argument(fullName="condition_on_depth", shortName="depth", doc="Condition validation on a minimum depth of coverage by the reads", required=false)
+    private int minDepth = -1;
 
-    @Output( doc="File to write the two-way truth table", required=false)
-    private PrintStream printStream = null;
 
     private String compName = "alleles";
     private UnifiedGenotyperEngine snpEngine;
@@ -115,6 +123,15 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
         if ( !rodList.get(0).getName().equals(compName))
             throw new UserException.BadInput("The ROD track has to be named \""+ compName +"\". Not " + rodList.get(0).getName());
 
+
+        // Initialize VCF header
+        Map<String, VCFHeader> header = VCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), compName);
+        Set<String> samples = SampleUtils.getSampleList(header, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
+        Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(header.values(), logger);
+        headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate"));
+        vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
+
+
         // Filling in SNP calling arguments for UG
         UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
         uac.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
@@ -143,7 +160,12 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
             return counter;
 
         VariantContext vcComp = tracker.getVariantContext(ref, compName, null, context.getLocation(), false);
-        if( vcComp == null ){
+        if( vcComp == null )
+            return counter;
+
+        // Do not operate on variants that are not covered to the optional minimum depth
+        if (!context.hasReads() || minDepth > 0 && context.getBasePileup().getBases().length < minDepth) {
+            counter.numUncovered = 1L;
             return counter;
         }
 
@@ -153,23 +175,22 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
         VariantCallContext call;
         if ( vcComp.isSNP() )
             call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
-        else if ( vcComp.isIndel() )
+        else if ( vcComp.isIndel() ) {
             call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
+            if (call.vc == null) // variant context will be null on an extended indel event and I just want to call it one event.
+                return counter;
+        }
         else {
             logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
             return counter;
         }
 
         if (!call.confidentlyCalled) {
-            if (context.hasReads()) {
-                counter.numNotConfidentCalls = 1L;
-                if (vcComp.getFilters().contains("TP"))
-                    counter.numFN = 1L;
-                else
-                    counter.numTN = 1L;
-            }
+            counter.numNotConfidentCalls = 1L;
+            if (vcComp.getFilters().contains("TP"))
+                counter.numFN = 1L;
             else
-                counter.numUncovered = 1L;
+                counter.numTN = 1L;
         }
         else {
             counter.numConfidentCalls = 1L;
@@ -178,7 +199,7 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
             else
                 counter.numFP = 1L;
         }
-
+        vcfWriter.add(vcComp, ref.getBase());
         return counter;
     }
 
@@ -202,6 +223,8 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
         logger.info("TN = " + reduceSum.numTN);
         logger.info("FP = " + reduceSum.numFP);
         logger.info("FN = " + reduceSum.numFN);
+        logger.info("PPV = " + ((double) reduceSum.numTP /( reduceSum.numTP + reduceSum.numFP)));
+        logger.info("FPV = " + ((double) reduceSum.numTN /( reduceSum.numTN + reduceSum.numFN)));
         logger.info("Uncovered = " + reduceSum.numUncovered);
         logger.info("confidently called = " + reduceSum.numConfidentCalls);
         logger.info("not confidently called = " + reduceSum.numNotConfidentCalls );