diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 3e7b5d2bd..6776798c3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -108,12 +108,6 @@ public class SelectVariants extends RodWalker { @Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't include filtered loci.", required=false) private boolean KEEP_ORIGINAL_CHR_COUNTS = false; - @Argument(fullName="discordance", shortName = "disc", doc="Output variants that were not called on a ROD comparison track", required=false) - private RodBinding discordanceTrack = RodBinding.makeUnbound(VariantContext.class); - - @Argument(fullName="concordance", shortName = "conc", doc="Output variants that were also called on a ROD comparison track", required=false) - private RodBinding concordanceTrack = RodBinding.makeUnbound(VariantContext.class); - @Hidden @Argument(fullName="keepAFSpectrum", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false) private boolean KEEP_AF_SPECTRUM = false; diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java index e864e5754..5e46f8f6f 100755 --- a/public/java/test/org/broadinstitute/sting/BaseTest.java +++ b/public/java/test/org/broadinstitute/sting/BaseTest.java @@ -64,7 +64,7 @@ public abstract class BaseTest { public static final String b37Refseq = refseqAnnotationLocation + "refGene-big-table-b37.txt"; public static final String dbsnpDataLocation = GATKDataLocation; - public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf"; + public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf"; public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf"; public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";