From 996a8b3cb3ae4e95350a8ab9cfa3f38d97b5410a Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Mon, 28 Jan 2019 14:52:51 -0500
Subject: [PATCH 1/2] Change default blocking and NON-REF LOD params for M2
 GVCF mode

---
 .../hellbender/tools/walkers/mutect/M2ArgumentCollection.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java
index 8a0c12de247..a35ea91d730 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java
@@ -251,12 +251,12 @@ public double getInitialLod() {
             "(must be specified in increasing order)", optional = true)
     public List<Double> GVCFGQBands = new ArrayList<>(70);
     {
-        for (double i = -4.0; i <= 1; i = i + 0.5) {
+        for (double i = -2.5; i <= 1; i = i + 0.5) {
             GVCFGQBands.add(i);
         }
     }
 
     @Advanced
     @Argument(fullName = "minimum-allele-fraction", shortName = "min-AF", doc = "Lower bound of variant allele fractions to consider when calculating variant LOD", optional = true)
-    public double minAF = 0.01;
+    public double minAF = 0.00;
 }

From 1f7d8956509f0b0a77298b8efc8d5c7e2b3413c7 Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Mon, 28 Jan 2019 15:16:53 -0500
Subject: [PATCH 2/2] Oops -- change tests to match

---
 .../tools/walkers/mutect/Mutect2IntegrationTest.java         | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java
index 1960c0b2eb5..8b0456365d2 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java
@@ -676,7 +676,8 @@ public void testMitochondrialRefConf() throws Exception {
                 "-O", standardVcf.getAbsolutePath(),
                 "-ERC", "GVCF",
                 "-LODB", "-2.0",
-                "-LODB", "0.0");
+                "-LODB", "0.0",
+                "-min-AF", "0.01");
         runCommandLine(args);
 
         //check ref conf-specific headers are output
@@ -718,7 +719,7 @@ public void testMitochondrialRefConf() throws Exception {
                 "-ERC", "GVCF",
                 "-LODB", "-2.0",
                 "-LODB", "0.0",
-                "-min-AF", "0.0");
+                "-min-AF", "0.00");
         runCommandLine(args3);
         final Pair<VCFHeader, List<VariantContext>> result_noThreshold = VariantContextTestUtils.readEntireVCFIntoMemory(unthresholded.getAbsolutePath());