diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/BcftoolsFillTagsStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/BcftoolsFillTagsStep.java
index 3016cf2c0..8feaa42dd 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/BcftoolsFillTagsStep.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/BcftoolsFillTagsStep.java
@@ -100,6 +100,7 @@ public VariantProcessingStep.Output processVariants(File inputVCF, File outputDi
             throw new PipelineJobException("No annotations were selected");
         }
 
+        options.add("--");
         options.add("-t");
         options.add(StringUtils.join(annotations, ","));