From 21dc9a55434eee8870956d504cfc0cc4a3167124 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Thu, 4 Aug 2011 12:31:28 -0400
Subject: [PATCH 1/2] Adding mills/devine indel dataset to the resource bundle

---
 .../sting/queue/qscripts/GATKResourcesBundle.scala             | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
index 934cf2a3c..4f1fe741a 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
@@ -134,6 +134,9 @@ class GATKResourcesBundle extends QScript {
     addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf",
       "1000G_indels_for_realignment", b37, true, false))
 
+    addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Mills_Devine_Indels_2011/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.vcf",
+      "indels_mills_devine", b37, true, true))
+    
     //
     // example call set for wiki tutorial
     //

From 98a96f07c163043586826b4d511f2efdc91bca1c Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Thu, 4 Aug 2011 14:06:26 -0400
Subject: [PATCH 2/2] Updated standard deviation parameter in VQSR to our
 current recommended value

---
 .../VariantRecalibratorArgumentCollection.java              | 2 +-
 .../VariantRecalibrationWalkersIntegrationTest.java         | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

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 e1a815913..28b279ccd 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
@@ -50,7 +50,7 @@ public class VariantRecalibratorArgumentCollection {
     @Argument(fullName="numKMeans", shortName="nKM", doc="The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model.", required=false)
     public int NUM_KMEANS_ITERATIONS = 30;
     @Argument(fullName="stdThreshold", shortName="std", doc="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model.", required=false)
-    public double STD_THRESHOLD = 8.0;
+    public double STD_THRESHOLD = 14.0;
     @Argument(fullName="qualThreshold", shortName="qual", doc="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model.", required=false)
     public double QUAL_THRESHOLD = 80.0;
     @Argument(fullName="shrinkage", shortName="shrinkage", doc="The shrinkage parameter in variational Bayes algorithm.", required=false)
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 057053a1c..3ac7e3785 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -26,9 +26,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     }
 
     VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
-            "d33212a84368e821cbedecd4f59756d6",  // tranches
-            "4652dca41222bebdf9d9fda343b2a835",  // recal file
-            "243a397a33a935fcaccd5deb6d16f0c0"); // cut VCF
+            "0ddd1e0e483d2eaf56004615cea23ec7",  // tranches
+            "58780f63182e139fdbe17f6c18b5b774",  // recal file
+            "f67d844b6252a55452cf4167b77530b1"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {