SAMtools up to 1.21.0 use after free

Summaryinfo

A vulnerability has been found in SAMtools up to 1.21.0 and classified as critical. Affected by this issue is some unknown functionality. Performing a manipulation results in use after free. This vulnerability is reported as CVE-2026-31972. The attack is possible to be carried out remotely. No exploit exists. The affected component should be upgraded.

Detailsinfo

A vulnerability was found in SAMtools up to 1.21.0. It has been classified as critical. This affects an unknown part. The manipulation with an unknown input leads to a use after free vulnerability. CWE is classifying the issue as CWE-416. Referencing memory after it has been freed can cause a program to crash, use unexpected values, or execute code. This is going to have an impact on confidentiality, integrity, and availability. The summary by CVE is:

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. 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. This bug is fixed in versions 1.21.1 and 1.22. There is no workaround for this issue.

It is possible to read the advisory at github.com. This vulnerability is uniquely identified as CVE-2026-31972 since 03/10/2026. The exploitability is told to be easy. It is possible to initiate the attack remotely. No form of authentication is needed for exploitation. The technical details are unknown and an exploit is not publicly available.

Upgrading to version 1.21.1 eliminates this vulnerability. Applying the patch 3036eb9af945fcef359427a2d359855553da4adf is able to eliminate this problem. The bugfix is ready for download at github.com. The best possible mitigation is suggested to be upgrading to the latest version.

The vulnerability is also documented in the vulnerability database at EUVD (EUVD-2026-12956). Statistical analysis made it clear that VulDB provides the best quality for vulnerability data.

Productinfo

Name

• SAMtools

Version

• 1.0
• 1.1
• 1.2
• 1.3
• 1.4
• 1.5
• 1.6
• 1.7
• 1.8
• 1.9
• 1.10
• 1.11
• 1.12
• 1.13
• 1.14
• 1.15
• 1.16
• 1.17
• 1.18
• 1.19
• 1.20
• 1.21.0

License

• open-source

Website

• Product: https://github.com/samtools/samtools/

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Statistical analysis made it clear that VulDB provides the best quality for vulnerability data.

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