From edbd17b8e048c49d8f2e2d287693091ff7e01fd4 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Tue, 23 Jul 2013 13:27:47 -0400 Subject: [PATCH] Added note of caution to VQSR gatkdocs for option BOTH of recalibration mode --- .../VariantRecalibratorArgumentCollection.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java index bdd41f37c..ae0b4a347 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java @@ -70,9 +70,9 @@ public class VariantRecalibratorArgumentCollection { throw new ReviewedStingException("VariantRecalibrator mode string is unrecognized, input = " + input); } - @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only snps (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both snps and indels simultaneously.", required = false) + @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels (emitting SNPs untouched in the output VCF); and 3.) BOTH for recalibrating both SNPs and indels simultaneously (for testing purposes only, not recommended for general use).", required = false) public VariantRecalibratorArgumentCollection.Mode MODE = VariantRecalibratorArgumentCollection.Mode.SNP; - @Argument(fullName="maxGaussians", shortName="mG", doc="The maximum number of Gaussians to try during variational Bayes algorithm", required=false) + @Argument(fullName="maxGaussians", shortName="mG", doc="The maximum number of Gaussians to try during variational Bayes algorithm.", required=false) public int MAX_GAUSSIANS = 10; @Argument(fullName="maxIterations", shortName="mI", doc="The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected.", required=false) public int MAX_ITERATIONS = 100;