--- a
+++ b/singlecellmultiomics/bamProcessing/bamReadGroupFormat.py
@@ -0,0 +1,79 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import argparse
+import pysam
+import sys
+from datetime import datetime
+import singlecellmultiomics
+from singlecellmultiomics.fragment import Fragment
+from singlecellmultiomics.bamProcessing.bamFunctions import get_read_group_from_read, sorted_bam_file, write_program_tag
+
+def set_read_group_format( in_bam_path, out_bam_path, format, threads=4  ):
+    """
+    Set read group format of bam file
+
+    Args:
+        in_bam_path(str) : bam file to read
+
+        in_bam_path(str) : bam file to write
+
+        format(int) : formatting mode, see `singlecellmultiomics.fragment.Fragment.get_read_group`
+
+        threads(int) : Amount of decompression threads for reading
+
+    """
+    read_groups = dict()  # Store unique read groups in this set
+    """
+    read_groups(set/dict) : set or dictionary which contains read groups. The dictionary should have the format { read_group_id (str)
+            { 'ID': ID, 'LB':library,
+            'PL':platform,
+            'SM':sampleLib,
+            'PU':readGroup }
+    """
+    with pysam.AlignmentFile(in_bam_path, threads = threads) as input_bam:
+
+        input_header = input_bam.header.as_dict()
+
+        # Write provenance information to BAM header
+        write_program_tag(
+            input_header,
+            program_name='bamReadGroupFormat',
+            command_line=" ".join(
+                sys.argv),
+            version=singlecellmultiomics.__version__,
+            description=f'SingleCellMultiOmics read group formatting, executed at {datetime.now().strftime("%d/%m/%Y %H:%M:%S")}')
+
+        with sorted_bam_file(out_bam_path, header=input_header, read_groups=read_groups, input_is_sorted=True) as out:
+            print('Started writing')
+            for read in input_bam:
+
+                rg_id = get_read_group_from_read(read, format=format,  with_attr_dict=False  )
+                if not rg_id in read_groups:
+                    rg_id, rg_data = get_read_group_from_read(read, format=format, with_attr_dict=True  )
+                    read_groups[rg_id] = rg_data
+
+                read.set_tag('RG',rg_id)
+                out.write(read)
+
+
+if __name__=='__main__':
+    argparser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        description='Change format of read groups')
+    argparser.add_argument('bamin', type=str)
+    argparser.add_argument(
+        '-format',
+        type=int,
+        default=0,
+        help="Read group format code")
+
+    argparser.add_argument(
+        '-t',
+        type=int,
+        default=4,
+        help="Threads")
+
+    argparser.add_argument('-o', type=str, help="output bam file", required=True)
+    args = argparser.parse_args()
+    set_read_group_format(args.bamin, args.o, args.format, args.t)