From 436b4dc855942cb1049af78d81be3fc2dce475ee Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 28 Nov 2011 08:59:48 -0500 Subject: [PATCH] Updated docs --- .../gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index c38bb5b42..c861af1a2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -50,11 +50,12 @@ public class UnifiedGenotyperEngine { public static final String LOW_QUAL_FILTER_NAME = "LowQual"; public enum OUTPUT_MODE { - /** the default */ + /** produces calls only at variant sites */ EMIT_VARIANTS_ONLY, - /** include confident reference sites */ + /** produces calls at variant sites and confident reference sites */ EMIT_ALL_CONFIDENT_SITES, - /** any callable site regardless of confidence */ + /** produces calls at any callable site regardless of confidence; this argument is intended for point + * mutations (SNPs) only and while some indel calls may be produced they are by no means comprehensive */ EMIT_ALL_SITES }