From ce4dc2128dc3146b71c3fffbd79024916efbfb4f Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Tue, 5 Jun 2012 15:17:56 -0400 Subject: [PATCH] Adding minor clarification to -mbq argument documentation --- .../sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java | 1 + 1 file changed, 1 insertion(+) 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 b33c036a8..599524026 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 @@ -100,6 +100,7 @@ public class UnifiedArgumentCollection { /** * The minimum confidence needed in a given base for it to be used in variant calling. Note that the base quality of a base * is capped by the mapping quality so that bases on reads with low mapping quality may get filtered out depending on this value. + * Note too that this argument is ignored in indel calling. In indel calling, low-quality ends of reads are clipped off (with fixed threshold of Q20). */ @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;