From 3ab2f4edb2e7fd4903ddd8f680e37f49e5c4a1d8 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Wed, 4 Dec 2013 19:55:24 -0500 Subject: [PATCH] Fixed documentation for -deletions argument in the UAC --- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 4fae3d6e3..04c5587c3 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -95,7 +95,11 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false) public int MIN_BASE_QUALTY_SCORE = 17; - @Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]", required = false) + /** + * If the fraction of reads with deletions spanning a locus is greater than this value, the site will not be considered callable and will be skipped. + * To disable the use of this parameter, set its value to >1. + */ + @Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable", required = false) public Double MAX_DELETION_FRACTION = 0.05; /**