Ensure VariantContexts are sorted in MergeVcfsAndGenotypes (#337)

BimberLab · Jul 29, 2024 · 8e61722 · 8e61722
1 parent f002b29
commit 8e61722
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/src/main/java/com/github/discvrseq/walkers/MergeVcfsAndGenotypes.java b/src/main/java/com/github/discvrseq/walkers/MergeVcfsAndGenotypes.java
@@ -340,6 +340,8 @@ else if (multipleAllelesMergeType == MultipleAllelesMergeType.MIX_TYPES) {
             logger.warn("Ignoring all records at site " + referenceContext.getContig() + ":" + referenceContext.getStart());
         }
 
+        // Ensure the result matches GATK's expected sort
+        mergedVCs.sort(new VariantContextComparator(getBestAvailableSequenceDictionary()));
         for ( final VariantContext mergedVC : mergedVCs ) {
             // only operate at the start of events
             if ( mergedVC == null )