From 077ea8f30c5950c1b3d225bca8ad7d7c7924a14e Mon Sep 17 00:00:00 2001
From: Menachem Fromer <fromer@broadinstitute.org>
Date: Wed, 9 Jan 2013 14:44:22 -0500
Subject: [PATCH] Added more options to control RBP behavior; raised default
 RBP PQ threshold to 20

---
 .../sting/gatk/walkers/phasing/ReadBackedPhasing.java           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
index ef84ed10b..d0b5fc5bd 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
@@ -117,7 +117,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
     protected Integer maxPhaseSites = 10; // 2^10 == 10^3 diploid haplotypes
 
     @Argument(fullName = "phaseQualityThresh", shortName = "phaseThresh", doc = "The minimum phasing quality score required to output phasing", required = false)
-    protected Double phaseQualityThresh = 10.0; // PQ = 10.0 <=> P(error) = 10^(-10/10) = 0.1, P(correct) = 0.9
+    protected Double phaseQualityThresh = 20.0; // PQ = 20.0 <=> P(error) = 10^(-20/10) = 0.01, P(correct) = 0.99
 
     @Hidden
     @Argument(fullName = "variantStatsFilePrefix", shortName = "variantStats", doc = "The prefix of the VCF/phasing statistics files [For DEBUGGING purposes only - DO NOT USE!]", required = false)