diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 36e4db1c5..41fa755b8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -138,7 +138,7 @@ public class IndelRealigner extends ReadWalker { * Any number of VCF files representing known indels to be used for constructing alternate consenses. * Could be e.g. dbSNP and/or official 1000 Genomes indel calls. Non-indel variants in these files will be ignored. */ - @Input(fullName="known", shortName = "known", doc="Input VCF file(s) with known indels", required=false) + @Input(fullName="knownAlleles", shortName = "known", doc="Input VCF file(s) with known indels", required=false) public List> known = Collections.emptyList(); /**