From a5a56f13158ccfc81469efd047a5b471ad332b24 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 28 Jul 2009 17:25:25 +0000
Subject: [PATCH] At this point, we are convinced that the new priors are the
 way to go...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1328 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/gatk/walkers/SingleSampleGenotyper.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
index 9e665b58a..1b06e1379 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
@@ -50,7 +50,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
     @Argument(fullName = "call_indels", shortName = "indels", doc = "Call indels as well as point mutations", required = false) public Boolean CALL_INDELS = false;
 
     // Control how the genotype hypotheses are weighed
-    @Argument(fullName = "priors_locus", shortName = "plocus", doc = "Comma-separated prior likelihoods for any locus (homref,het,homvar)", required = false) public String PRIORS_ANY_LOCUS = "0.999,1e-3,1e-5";
+    @Argument(fullName = "priors_locus", shortName = "plocus", doc = "Comma-separated prior likelihoods for any locus (homref,het,homvar)", required = false) public String PRIORS_ANY_LOCUS = "0.999,0.000333,0.000667";
     @Argument(fullName = "priors_hapmap", shortName = "phapmap", doc = "Comma-separated prior likelihoods for Hapmap loci (homref,het,homvar)", required = false) public String PRIORS_HAPMAP = "0.999,1e-3,1e-5";
     @Argument(fullName = "priors_dbsnp", shortName = "pdbsnp", doc = "Comma-separated prior likelihoods for dbSNP loci (homref,het,homvar)", required = false) public String PRIORS_DBSNP = "0.999,1e-3,1e-5";
     @Argument(fullName = "priors_2nd_on", shortName = "p2ndon", doc = "Comma-separated prior likelihoods for the secondary bases of primary on-genotype bases (AA,AC,AG,AT,CC,CG,CT,GG,GT,TT)", required = false) public String PRIORS_2ND_ON = "0.000,0.302,0.366,0.142,0.000,0.548,0.370,0.000,0.319,0.000";