diff --git a/src/read_groups.py b/src/read_groups.py
index 78a7d8eb..b141966b 100644
--- a/src/read_groups.py
+++ b/src/read_groups.py
@@ -186,7 +186,8 @@ def split_read_group_table(table_file, sample, read_id_column_index, group_id_co
     for bam_file in bam_files:
         bam = pysam.AlignmentFile(bam_file, "rb")
         for chr_id in bam.references:
-            read_group_files[chr_id] = open(sample.read_group_file + "_" + chr_id, "w")
+            if chr_id not in read_group_files:
+                read_group_files[chr_id] = open(sample.read_group_file + "_" + chr_id, "w")
         for read_alignment in bam:
             chr_id = read_alignment.reference_name
             if not chr_id: