samtools: NULL Pointer Dereference
CVE-2026-31973 is a high-severity NULL pointer dereference vulnerability in samtools, with a CVSS 3.1 base score of 7.5 out of 10. It can be exploited remotely over the network by an unauthenticated attacker, without any action from a user. Affected samtools versions: >= 1.17, < 1.21.1; >= 1.22, < 1.22.2; = 1.23. The record does not name a fixed version, so check the vendor advisory. There is no confirmed exploitation so far. EPSS estimates a 0.59% chance of exploitation within 30 days, which is low compared with other CVEs.
High severity with no evidence of exploitation so far.
What to do
- Check which version of samtools you run against the affected versions below, and install the vendor's latest release.
- Read the advisory on github.com for workarounds and exact fixed builds.
- Until you can update, restrict network access to the affected service so it is not reachable from untrusted networks.
Affected products and versions
| Vendor | Product | Affected versions | Fixed in |
|---|---|---|---|
| Samtools | samtools | >= 1.17, < 1.21.1; >= 1.22, < 1.22.2; = 1.23 | Not stated |
Version data comes from the organisation that assigned the CVE. Confirm against the vendor advisory before deciding you are unaffected.
How the severity score breaks down
- Attack vector
- NetworkCan be exploited remotely over a network, including the internet.
- Attack complexity
- LowNo special conditions are needed; the attack works reliably.
- Privileges required
- NoneNo account or login is needed.
- User interaction
- NoneNo action by a victim is required.
- Scope
- UnchangedImpact stays within the vulnerable component.
- Confidentiality
- NoneNo data is disclosed.
- Integrity
- NoneNothing can be modified.
- Availability
- HighThe component can be taken down completely.
Vector: CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:N/A:H. Scored by NVD.
| Scoring system | Score | Severity | Scored by |
|---|---|---|---|
| CVSS 4.0 | 6.9 | Medium | CNA (github.com) |
| CVSS 3.1 | 7.5 | High | NVD |
Official description
SAMtools is a program for reading, manipulating and writing bioinformatics file formats. Starting in version 1.17, in the cram-size command, used to write information about how well CRAM files are compressed, a check to see if the `cram_decode_compression_header()` was missing. If the function returned an error, this could lead to a NULL pointer dereference. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.
Source: the CVE record as published by its numbering authority, via NVD and CVE.org.
The underlying weakness: NULL Pointer Dereference
The product dereferences a pointer that it expects to be valid but is NULL.
How developers prevent this class of flaw
- For any pointers that could have been modified or provided from a function that can return NULL, check the pointer for NULL before use. When working with a multithreaded or otherwise asynchronous environment, ensure that proper locking APIs are used to lock before the check, and unlock when it has finished.
- Select a programming language that is not susceptible to these issues.
- Check the results of all functions that return a value and verify that the value is non-null before acting upon it.
Timeline
- CVE record published.
- CISA published its SSVC assessment (exploitation: none, automatable: no, technical impact: partial).
- Record last changed materially (score, affected products, status or references).
References
Patches and release notes
Third-party and government advisories
- openwall.com/lists/oss-security/2026/03/18/12Mailing List, Third Party Advisory
Other vulnerabilities in samtools
- 9.8 Critical severity
Recent NULL Pointer Dereference vulnerabilities
- 7.5 High severity
- 7.5 High severity
- 7.8 High severity
- 7.5 High severity
- 7.5 High severity
- 7.5 High severity
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