# CVE-2026-31972: samtools: SAMtools is a program for reading, manipulating and writing bioinformatics file formats

CVE-2026-31972 is fixed in samtools on 1 platform by DEBIAN-CVE-2026-31972 (version 1.24-2), released March 18, 2026. It is not reported as exploited. Patch Radar priority: Urgent.

- Web page: https://patchblox.com/security/cve/CVE-2026-31972
- Priority: Urgent
- CVSS: 9.8 (critical)
- EPSS: 0.0055
- CISA KEV: not listed
- Exploited (vendor report): no
- Publicly disclosed: no
- Published: Mar 18, 2026

## 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. 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.

## Where it's fixed

| Platform | Product | Fixed in | Fix | Released |
|---|---|---|---|---|
| Linux | samtools Debian 14 | 1.24-2 | [DEBIAN-CVE-2026-31972](https://patchblox.com/security/data/fix/linux/debian-cve-2026-31972.md) | Mar 18, 2026 |

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Data as of 2026-11-08T13:06:02Z UTC. Source: Patchblox Patch Radar (https://patchblox.com/security/patch-radar). Patchblox finds out-of-date software on Windows, macOS and Linux and updates it through release rings: https://patchblox.com/demo

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