From 546b5e565ff71cd7dfbe8975b76da3a1837e0488 Mon Sep 17 00:00:00 2001
From: michaelgatzen <mgatzen@broadinstitute.org>
Date: Thu, 11 Jan 2024 11:34:31 -0500
Subject: [PATCH] MarkDuplicates: Add read group ID instead of string "RG"
 (#1937)

* fixes https://github.com/broadinstitute/picard/issues/1936
---
 src/main/java/picard/sam/markduplicates/MarkDuplicates.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/picard/sam/markduplicates/MarkDuplicates.java b/src/main/java/picard/sam/markduplicates/MarkDuplicates.java
index bcde79a5ff..b1ad890eae 100644
--- a/src/main/java/picard/sam/markduplicates/MarkDuplicates.java
+++ b/src/main/java/picard/sam/markduplicates/MarkDuplicates.java
@@ -555,7 +555,7 @@ private void buildSortedReadEndLists(final boolean useBarcodes) {
 
                 if (rec.getReadPairedFlag() && !rec.getMateUnmappedFlag()) {
                     final StringBuilder key = new StringBuilder();
-                    key.append(ReservedTagConstants.READ_GROUP_ID);
+                    key.append(rec.getReadGroup().getReadGroupId());
                     key.append(rec.getReadName());
                     ReadEndsForMarkDuplicates pairedEnds = tmp.remove(rec.getReferenceIndex(), key.toString());