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misc minor bug fixes in assembly. Increasing the minimum number of bad variants to be used in negative model training in the VQSR

This commit is contained in:
Ryan Poplin 2011-08-29 08:11:31 -04:00
parent f9afc5876a
commit bc252a0d62
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
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@ -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) @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; 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) @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;
} }