From d6e1205310324e6c468543205a9676138b4404c1 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Wed, 30 May 2012 10:48:45 -0400 Subject: [PATCH] Updating default values for DiagnoseTargets --- .../gatk/walkers/diagnostics/targets/DiagnoseTargets.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java index b8a90892f..10306b116 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java @@ -102,10 +102,10 @@ public class DiagnoseTargets extends LocusWalker { private int maximumCoverage = 700; @Argument(fullName = "minimum_median_depth", shortName = "med", doc = "The minimum allowable median coverage, used for calling LOW_MEDIAN_DEPTH", required = false) - private int minMedianDepth = 20; + private int minMedianDepth = 10; @Argument(fullName = "maximum_insert_size", shortName = "ins", doc = "The maximum allowed distance between a read and its mate", required = false) - private int maxInsertSize = 50; + private int maxInsertSize = 500; @Argument(fullName = "voting_status_threshold", shortName = "stV", doc = "The needed percentage of samples containing a call for the interval to adopt the call ", required = false) private double votePercentage = 0.50;