From 1cb5e9e149161e88890a74fb4d1f523c7313b139 Mon Sep 17 00:00:00 2001 From: Laurent Francioli Date: Wed, 30 Nov 2011 14:45:04 +0100 Subject: [PATCH] Removed outdated (and unused) -familyStr commandline argument --- .../sting/gatk/walkers/annotator/VariantAnnotator.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 143f2eb2e..94902e828 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -167,9 +167,6 @@ public class VariantAnnotator extends RodWalker implements Ann @Argument(fullName="vcfContainsOnlyIndels", shortName="dels",doc="Use if you are annotating an indel vcf, currently VERY experimental", required = false) protected boolean indelsOnly = false; - @Argument(fullName="family_string",shortName="family",required=false,doc="A family string of the form mom+dad=child for use with the mendelian violation ratio annotation") - public String familyStr = null; - @Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="The genotype quality treshold in order to annotate mendelian violation ratio") public double minGenotypeQualityP = 0.0;