@@ -41,7 +43,7 @@ class ApplyRecalibration(val parent: Configurable) extends CommandLineGATK with
/** The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value */
@Output(fullName="out",shortName="o",doc="The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value",required=false,exclusiveOf="",validation="")
@Gather(classOf[CatVariantsGatherer])
@Gather(classOf[GatherVcfs])
varout:File=_
/** The truth sensitivity level at which to start filtering */
@@ -29,7 +31,7 @@ class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with Sca
/** File to which variants should be written */
@Output(fullName="out",shortName="o",doc="File to which variants should be written",required=false,exclusiveOf="",validation="")
@Gather(classOf[CatVariantsGatherer])
@Gather(classOf[GatherVcfs])
varout:File=_
/** What likelihood calculation engine to use to calculate the relative likelihood of reads vs haplotypes */
...
...
@@ -96,7 +98,7 @@ class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with Sca
/** File to which assembled haplotypes should be written */
@Output(fullName="bamOutput",shortName="bamout",doc="File to which assembled haplotypes should be written",required=false,exclusiveOf="",validation="")