diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java
index bce9d08f0..1c34d1e14 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java
@@ -124,6 +124,11 @@ public boolean scatterMethodRequiresSort()
             return false;
         }
 
+        if (getParameterJson().optBoolean("scatterGather.forceVcfSort", false))
+        {
+            return true;
+        }
+
         return !doAllowSplitContigs();
     }