Version

$ samtools --version
samtools 1.22.1
Using htslib 1.22.1
Copyright (C) 2025 Genome Research Ltd.

Version 1.22.1 (build h96c455f_0) from Bioconda.

Environment

• Debian 12 Linux amd64

Reproduce

Duplicate tags are forbidden as of SAM v1.6:

Within each (non-@CO) header line, no field tag may appear more than once and the order in which the fields appear is not significant.

Using the following SAM file does not raise any error with samtools:

@HD	VN:1.6	SO:coordinate
@RG	ID:rg1	DS:desc1	DS:desc2
@SQ	SN:ref	LN:45
r001	99	ref	7	30	8M2I4M1D3M	=	37	39	TTAGATAAAGGATACTG	*	RG:Z:rg1

$ samtools quickcheck test.sam
$ echo $?
0
$ samtools view -b test.sam > /dev/null
$ echo $?
0

See also a related issue first raised with noodles: zaeleus/noodles#352