diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java index b58e5ce18..8f1ba6c2d 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java @@ -65,7 +65,7 @@ public class ApplyVariantCuts extends RodWalker { private String TRANCHE_FILENAME = "optimizer.dat.tranches"; @Argument(fullName="outputVCFFile", shortName="outputVCF", doc="The output filtered VCF file", required=true) private String OUTPUT_FILENAME = "optimizer.vcf"; - @Argument(fullName="fdr_filter_level", shortName="fdr_filter_level", doc="The FDR level at which to start filtering.", required=true) + @Argument(fullName="fdr_filter_level", shortName="fdr_filter_level", doc="The FDR level at which to start filtering.", required=false) private double FDR_FILTER_LEVEL = 0.0;