From 8e61722b9368da0c79dd6dc64fca604e8c4bea64 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Sun, 28 Jul 2024 20:41:07 -0500
Subject: [PATCH] Ensure VariantContexts are sorted in MergeVcfsAndGenotypes
 (#337)

---
 .../com/github/discvrseq/walkers/MergeVcfsAndGenotypes.java     | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/main/java/com/github/discvrseq/walkers/MergeVcfsAndGenotypes.java b/src/main/java/com/github/discvrseq/walkers/MergeVcfsAndGenotypes.java
index 758ac06d..89b4c47a 100644
--- 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 )