This argument should be annotated as @Input
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@ -130,7 +130,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
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// boolean FORMAT_VCF = false;
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@Hidden
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@Argument(fullName = "genotype_intervals", shortName = "genotype",
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@Input(fullName = "genotype_intervals", shortName = "genotype",
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doc = "Calls will be made at each position within the specified interval(s), whether there is an indel or not", required = false)
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public IntervalBinding<Feature> genotypeIntervalsFile = null;
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