From bc252a0d62f699afe66520b1f693a83895477ad1 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Mon, 29 Aug 2011 08:11:31 -0400
Subject: [PATCH 2/7] misc minor bug fixes in assembly. Increasing the minimum
 number of bad variants to be used in negative model training in the VQSR

---
 .../VariantRecalibratorArgumentCollection.java                  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
index a0920113b..df396b714 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
@@ -62,5 +62,5 @@ public class VariantRecalibratorArgumentCollection {
     @Argument(fullName="percentBadVariants", shortName="percentBad", doc="What percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent.", required=false)
     public double PERCENT_BAD_VARIANTS = 0.03;
     @Argument(fullName="minNumBadVariants", shortName="minNumBad", doc="The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad argument if necessary.", required=false)
-    public int MIN_NUM_BAD_VARIANTS = 2000;
+    public int MIN_NUM_BAD_VARIANTS = 2500;
 }

From bb7a37e8f2c8911f95ccacf305175cf30bca0302 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 29 Aug 2011 13:19:35 -0400
Subject: [PATCH 5/7] We need to allow reference calls in the input VCF for the
 GenotypeAndValidate walker when using the BAM as truth so that we can test
 supposed monomorphic calls against the truth.

---
 .../walkers/validation/GenotypeAndValidateWalker.java  | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
index 2b38afaf6..00a506fab 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
@@ -347,12 +347,14 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
         }
 
         VariantCallContext call;
-        if ( vcComp.isSNP() )
+        if ( vcComp.isSNP() ) {
             call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
-        else if ( vcComp.isIndel() ) {
+        } else if ( vcComp.isIndel() ) {
             call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
-        }
-        else {
+        } else if ( bamIsTruth ) {
+            // assume it's a SNP if no variation is present; this is necessary so that we can test supposed monomorphic sites against the truth bam
+            call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
+        } else {
             logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
             return counter;
         }

From c2f0db969b91b323c2fc991cc6319afb9c3f9fc6 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 29 Aug 2011 13:48:10 -0400
Subject: [PATCH 6/7] Don't use the default deletion value from UG if not
 asking to have it set

---
 .../gatk/walkers/validation/GenotypeAndValidateWalker.java   | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
index 00a506fab..b616a0ebe 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
@@ -303,7 +303,10 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
         uac.alleles = alleles;
         if (!bamIsTruth) uac.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
         if (mbq >= 0) uac.MIN_BASE_QUALTY_SCORE = mbq;
-        if (deletions >= 0) uac.MAX_DELETION_FRACTION = deletions;
+        if (deletions >= 0)
+            uac.MAX_DELETION_FRACTION = deletions;
+        else
+            uac.MAX_DELETION_FRACTION = 1.0;
         if (emitConf >= 0) uac.STANDARD_CONFIDENCE_FOR_EMITTING = emitConf;
         if (callConf >= 0) uac.STANDARD_CONFIDENCE_FOR_CALLING = callConf;