From bc252a0d62f699afe66520b1f693a83895477ad1 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 29 Aug 2011 08:11:31 -0400 Subject: [PATCH] misc minor bug fixes in assembly. Increasing the minimum number of bad variants to be used in negative model training in the VQSR --- .../VariantRecalibratorArgumentCollection.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java index a0920113b..df396b714 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java @@ -62,5 +62,5 @@ public class VariantRecalibratorArgumentCollection { @Argument(fullName="percentBadVariants", shortName="percentBad", doc="What percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent.", required=false) public double PERCENT_BAD_VARIANTS = 0.03; @Argument(fullName="minNumBadVariants", shortName="minNumBad", doc="The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad argument if necessary.", required=false) - public int MIN_NUM_BAD_VARIANTS = 2000; + public int MIN_NUM_BAD_VARIANTS = 2500; }