From d6e1205310324e6c468543205a9676138b4404c1 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Wed, 30 May 2012 10:48:45 -0400 Subject: [PATCH 1/2] 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; From d09b8d55841c7308d33c82beaa55a0ff6ed6ca67 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 30 May 2012 13:24:08 -0400 Subject: [PATCH 2/2] Fixing docs --- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 89b659ef8..ca59ae452 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -37,7 +37,8 @@ public class UnifiedArgumentCollection { /** * Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus. */ - @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ -- EXACT is the default option, while GRID_SEARCH is also available.", required = false) + @Advanced + @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false) protected AlleleFrequencyCalculationModel.Model AFmodel = AlleleFrequencyCalculationModel.Model.EXACT; /**