diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/VariantProcessingStep.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/VariantProcessingStep.java
index e8ca43357..34887620a 100644
--- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/VariantProcessingStep.java
+++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/VariantProcessingStep.java
@@ -45,10 +45,22 @@ default void complete(PipelineJob job, List<SequenceOutputFile> inputs, List<Seq
 
     enum ScatterGatherMethod
     {
-        none(),
-        contig(),
-        chunked(),
-        fixedJobs()
+        none(false),
+        contig(false),
+        chunked(true),
+        fixedJobs(false);
+
+        private final boolean _mayRequireSort;
+
+        ScatterGatherMethod(boolean mayRequireSort)
+        {
+            _mayRequireSort = mayRequireSort;
+        }
+
+        public boolean mayRequireSort()
+        {
+            return _mayRequireSort;
+        }
     }
 
     interface Output extends PipelineStepOutput
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java
index 088e952b1..bce9d08f0 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java
@@ -117,6 +117,16 @@ private void validateScatterForTask()
         sg.validateScatter(getScatterGatherMethod(), this);
     }
 
+    public boolean scatterMethodRequiresSort()
+    {
+        if (_scatterGatherMethod == null || !_scatterGatherMethod.mayRequireSort())
+        {
+            return false;
+        }
+
+        return !doAllowSplitContigs();
+    }
+
     private LinkedHashMap<String, List<Interval>> establishIntervals()
     {
         LinkedHashMap<String, List<Interval>> ret;
@@ -137,7 +147,7 @@ else if (_scatterGatherMethod == VariantProcessingStep.ScatterGatherMethod.chunk
             getLogger().info("Creating jobs with target bp size: " + basesPerJob + " mbp.  allow splitting configs: " + allowSplitChromosomes + ", max contigs per job: " + maxContigsPerJob);
 
             basesPerJob = basesPerJob * 1000000;
-            ret = ScatterGatherUtils.divideGenome(dict, basesPerJob, allowSplitChromosomes, maxContigsPerJob);
+            ret = ScatterGatherUtils.divideGenome(dict, basesPerJob, allowSplitChromosomes, maxContigsPerJob, scatterMethodRequiresSort());
 
         }
         else if (_scatterGatherMethod == VariantProcessingStep.ScatterGatherMethod.fixedJobs)
@@ -146,7 +156,7 @@ else if (_scatterGatherMethod == VariantProcessingStep.ScatterGatherMethod.fixed
             int numJobs = getParameterJson().getInt("scatterGather.totalJobs");
             int jobSize = (int)Math.ceil(totalSize / (double)numJobs);
             getLogger().info("Creating " + numJobs + " jobs with approximate size: " + jobSize + " bp.");
-            ret = ScatterGatherUtils.divideGenome(dict, jobSize, true, -1);
+            ret = ScatterGatherUtils.divideGenome(dict, jobSize, true, -1, false);
         }
         else
         {
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingRemoteMergeTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingRemoteMergeTask.java
index f962a73cc..5eeb8e50e 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingRemoteMergeTask.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingRemoteMergeTask.java
@@ -222,7 +222,7 @@ else if (!vcf.exists())
                     throw new PipelineJobException("Missing one of more VCFs: " + missing.stream().map(File::getPath).collect(Collectors.joining(",")));
                 }
 
-                boolean sortAfterMerge = handler instanceof VariantProcessingStep.SupportsScatterGather && ((VariantProcessingStep.SupportsScatterGather) handler).doSortAfterMerge();
+                boolean sortAfterMerge = getPipelineJob().scatterMethodRequiresSort() || handler instanceof VariantProcessingStep.SupportsScatterGather && ((VariantProcessingStep.SupportsScatterGather) handler).doSortAfterMerge();
                 combined = SequenceAnalysisService.get().combineVcfs(toConcat, combined, genome, getJob().getLogger(), true, null, sortAfterMerge);
             }
             manager.addOutput(action, "Merged VCF", combined);
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ScatterGatherUtils.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ScatterGatherUtils.java
index 4affbe7e2..8e69a3553 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ScatterGatherUtils.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ScatterGatherUtils.java
@@ -7,7 +7,6 @@
 import org.junit.Test;
 
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
@@ -113,13 +112,17 @@ private void addInterval(String refName, int start, int end)
         }
     }
 
-    public static LinkedHashMap<String, List<Interval>> divideGenome(SAMSequenceDictionary dict, int optimalBasesPerJob, boolean allowSplitChromosomes, int maxContigsPerJob)
+    public static LinkedHashMap<String, List<Interval>> divideGenome(SAMSequenceDictionary dict, int optimalBasesPerJob, boolean allowSplitChromosomes, int maxContigsPerJob, boolean sortOnContigSize)
     {
         ActiveIntervalSet ais = new ActiveIntervalSet(optimalBasesPerJob, allowSplitChromosomes, maxContigsPerJob);
 
         // Sort the sequences in descending length, rather than alphabetic on name:
         List<SAMSequenceRecord> sortedSeqs = new ArrayList<>(dict.getSequences());
-        sortedSeqs.sort(Comparator.comparingInt(SAMSequenceRecord::getSequenceLength).reversed());
+        if (sortOnContigSize)
+        {
+            sortedSeqs.sort(Comparator.comparingInt(SAMSequenceRecord::getSequenceLength).reversed());
+        }
+
         for (SAMSequenceRecord rec : sortedSeqs)
         {
             ais.add(rec);
@@ -152,13 +155,13 @@ private SAMSequenceDictionary getDict()
         public void testScatter()
         {
             SAMSequenceDictionary dict = getDict();
-            Map<String, List<Interval>> ret = divideGenome(dict, 1000, true, -1);
+            Map<String, List<Interval>> ret = divideGenome(dict, 1000, true, -1, true);
             assertEquals("Incorrect number of jobs", 8, ret.size());
             assertEquals("Incorrect interval end", 1000, ret.get("Job3").get(0).getEnd());
             assertEquals("Incorrect start", 1, ret.get("Job3").get(0).getStart());
             assertEquals("Incorrect interval end", 4, ret.get("Job8").size());
 
-            Map<String, List<Interval>> ret2 = divideGenome(dict, 3000, false, -1);
+            Map<String, List<Interval>> ret2 = divideGenome(dict, 3000, false, -1, true);
             assertEquals("Incorrect number of jobs", 3, ret2.size());
             for (String jobName : ret2.keySet())
             {
@@ -168,7 +171,7 @@ public void testScatter()
                 }
             }
 
-            Map<String, List<Interval>> ret3 = divideGenome(dict, 3002, false, -1);
+            Map<String, List<Interval>> ret3 = divideGenome(dict, 3002, false, -1, true);
             assertEquals("Incorrect number of jobs", 3, ret3.size());
             for (String jobName : ret3.keySet())
             {
@@ -178,7 +181,7 @@ public void testScatter()
                 }
             }
 
-            Map<String, List<Interval>> ret4 = divideGenome(dict, 2999, false, -1);
+            Map<String, List<Interval>> ret4 = divideGenome(dict, 2999, false, -1, true);
             assertEquals("Incorrect number of jobs", 3, ret4.size());
             for (String jobName : ret4.keySet())
             {
@@ -188,7 +191,7 @@ public void testScatter()
                 }
             }
 
-            Map<String, List<Interval>> ret5 = divideGenome(dict, 750, true, -1);
+            Map<String, List<Interval>> ret5 = divideGenome(dict, 750, true, -1, true);
             assertEquals("Incorrect number of jobs", 9, ret5.size());
             assertEquals("Incorrect interval end", 750, ret5.get("Job1").get(0).getEnd());
             assertEquals("Incorrect interval end", 4, ret5.get("Job9").size());
@@ -196,7 +199,7 @@ public void testScatter()
             assertEquals("Incorrect interval start", 1501, ret5.get("Job3").get(0).getStart());
             assertEquals("Incorrect interval start", 1, ret5.get("Job8").get(0).getStart());
 
-            Map<String, List<Interval>> ret6 = divideGenome(dict, 5000, false, 2);
+            Map<String, List<Interval>> ret6 = divideGenome(dict, 5000, false, 2, true);
             assertEquals("Incorrect number of jobs", 5, ret6.size());
         }
     }