@@ -180,7 +140,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
/** The minimum phred-scaled confidence threshold at which variants should be called */
@Argument(fullName="standard_min_confidence_threshold_for_calling",shortName="stand_call_conf",doc="The minimum phred-scaled confidence threshold at which variants should be called",required=false,exclusiveOf="",validation="")
/** Format string for standard_min_confidence_threshold_for_calling */
@Argument(fullName="standard_min_confidence_threshold_for_callingFormat",shortName="",doc="Format string for standard_min_confidence_threshold_for_calling",required=false,exclusiveOf="",validation="")
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@@ -188,7 +148,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
/** The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold) */
@Argument(fullName="standard_min_confidence_threshold_for_emitting",shortName="stand_emit_conf",doc="The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)",required=false,exclusiveOf="",validation="")
/** Format string for standard_min_confidence_threshold_for_emitting */
@Argument(fullName="standard_min_confidence_threshold_for_emittingFormat",shortName="",doc="Format string for standard_min_confidence_threshold_for_emitting",required=false,exclusiveOf="",validation="")
/** Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context */
@Argument(fullName="sample",shortName="sn",doc="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context",required=false,exclusiveOf="",validation="")
/** Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets */
@Argument(fullName="known_names",shortName="knownName",doc="Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets",required=false,exclusiveOf="",validation="")