oss-security - CVE-2026-31972: samtools <= 1.21 Use-after-free in mpileup leading to an invalid read

Follow @Openwall on Twitter for new release announcements and other news

[<prev] [next>] [day] [month] [year] [list]

Message-ID: <alpine.DEB.2.21.2603182111000.16613@seq4-head1.internal.sanger.ac.uk>
Date: Wed, 18 Mar 2026 21:11:51 +0000 (GMT)
From: Robert Davies <rmd@...ger.ac.uk>
To: oss-security@...ts.openwall.com
cc: samtools@...ger.ac.uk
Subject: CVE-2026-31972: samtools <= 1.21 Use-after-free in mpileup leading
 to an invalid read

Description
-----------

SAMtools is a program for reading, manipulating and writing bioinformatics
file formats. The "mpileup" command outputs DNA sequences that have been
aligned against a known reference. On each output line it writes the
reference position, optionally the reference DNA base at that position
(obtained from a separate file) and all of the DNA bases that aligned to
that position. As the output is ordered by position, reference data that is
no longer needed is discarded once it has been printed out. Under certain
conditions the data could be discarded too early, leading to an attempt to
read from a pointer to freed memory.

Impact
------

This bug may allow information about program state to be leaked. It may also
cause a program crash through an attempt to access invalid memory.

Severity
--------

Moderate CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N

Patches
-------

This bug is fixed in versions 1.21.1 and 1.22

Workarounds
-----------

There is no workaround for this issue.

References
----------

https://github.com/samtools/samtools/security/advisories/GHSA-72c8-4jf3-f27p
https://www.cve.org/CVERecord?id=CVE-2026-31972

-- 

The SAMtools team   https://www.htslib.org/  https://www.sanger.ac.uk/

----------------------------------------------------------------------
The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA.

Please check out the Open Source Software Security Wiki, which is counterpart to this mailing list.

Confused about mailing lists and their use? Read about mailing lists on Wikipedia and check out these guidelines on proper formatting of your messages.