VulnerabilityPublished 18 Mar 2026

CVE-2026-31964: samtools htslib · NULL Pointer Dereference

Affects samtools htslibSource CVE Database V5

Compare

Not known to be exploited · CVSS 6.9 Medium : upgrade to 1.22.2 or 1.21.1 when convenient.

Data as of 30 Oct 2026, 06:59 UTC

CVSS 4.0 base score

6.9Medium

How severe the flaw is on the 0–10 CVSS scale.

EPSS: 0.3% chance of exploitation in 30 days – higher than 26% of CVEsExploit Prediction Scoring System: the likelihood attackers will use this flaw soon.
Patch: Available – fixed in 1.22.2, 1.21.1

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

Attack Vector: Network
Attack Complexity: Low
Attack Requirements: None
Privileges Required: None
User Interaction: None
Vulnerable system confidentiality: None
Vulnerable system integrity: Low
Vulnerable system availability: Low
Subsequent system confidentiality: None
Subsequent system integrity: None
Subsequent system availability: None

Bold values are the worst case: easiest to exploit or largest impact.

Attack Vector: Network: The vulnerable system is bound to the network stack and the set of possible attackers extends beyond the other options listed below, up to and including the entire Internet. Such a vulnerability is often termed “remotely exploitable” and can be thought of as an attack being exploitable at the protocol level one or more network hops away (e.g., across one or more routers).
Attack Complexity: Low: The attacker must take no measurable action to exploit the vulnerability. The attack requires no target-specific circumvention to exploit the vulnerability. An attacker can expect repeatable success against the vulnerable system.
Attack Requirements: None: The successful attack does not depend on the deployment and execution conditions of the vulnerable system. The attacker can expect to be able to reach the vulnerability and execute the exploit under all or most instances of the vulnerability.
Privileges Required: None: The attacker is unauthorized prior to attack, and therefore does not require any access to settings or files of the vulnerable system to carry out an attack.
User Interaction: None: The vulnerable system can be exploited without interaction from any human user, other than the attacker.
Vulnerable system confidentiality: None: There is no loss of confidentiality within the Vulnerable System.
Vulnerable system integrity: Low: Modification of data is possible, but the attacker does not have control over the consequence of a modification, or the amount of modification is limited. The data modification does not have a direct, serious impact to the Vulnerable System.
Vulnerable system availability: Low: Performance is reduced or there are interruptions in resource availability. Even if repeated exploitation of the vulnerability is possible, the attacker does not have the ability to completely deny service to legitimate users. The resources in the Vulnerable System are either partially available all of the time, or fully available only some of the time, but overall there is no direct, serious consequence to the Vulnerable System.
Subsequent system confidentiality: None: There is no loss of confidentiality within the Subsequent System or all confidentiality impact is constrained to the Vulnerable System.
Subsequent system integrity: None: There is no loss of integrity within the Subsequent System or all integrity impact is constrained to the Vulnerable System.
Subsequent system availability: None: There is no impact to availability within the Subsequent System or all availability impact is constrained to the Vulnerable System.

Definitions: FIRST CVSS v4.0 specification.

Exploitation evidence

Disclosed: evidence found.
CVE published 18 Mar 2026
Detectable: no evidence on record.
No public nuclei template indexed
Weaponized: no evidence on record.
No public exploit code indexed in Metasploit or Exploit-DB
Exploited in the wildExploited: no evidence on record.
Not in CISA KEV and no source reports exploitation
Observed by OffSeq MirageSeen by Mirage: no evidence on record.
No attack traffic recorded by OffSeq Mirage sensors

A missing step is not evidence of safety. Sources: cve.org (opens in a new tab), the Metasploit, Exploit-DB and nuclei-templates index as of 29 Oct 2026.

Disclosed: The CVE record is public on cve.org. Its publication is t = 0.
Detectable: A public nuclei template can find exposed instances, for defenders and attackers alike.
Weaponized: A Metasploit exploit module or Exploit-DB entry exists (Metasploit scanner modules do not count), or CISA SSVC or the CVSS exploit maturity reports a public proof of concept.
Exploited in the wild: CISA KEV lists it, CISA SSVC rates exploitation active, or a source reports attacks.
Observed by OffSeq Mirage: OffSeq Mirage honeypot sensors recorded attack traffic for this CVE, or found exposed hosts without attack traffic.

Moments are spaced evenly, not to scale; a dashed line marks a gap of six months or more. Deltas count from t = 0. Sources that give only a date (CISA KEV, Exploit-DB, or a time of exactly 00:00Z) read “same day” rather than hours. Metasploit modules carry the flaw’s disclosure date, not their release date, and nuclei templates carry no date, so both appear above but not on the timeline.

What to do

Upgrade htslib to 1.22.2 or 1.21.1; samtools/htslib to 1.21.1.

Affected software

Product	Affected	Fixed in
samtoolshtslib	Affected <1.21.1 >=1.22 <1.22.2 =1.23	Fixed in 1.22.2 1.21.1
GitHubsamtools/htslib`pkg:github/samtools/htslib`Other threats	Affected <1.21.1 =1.23	Fixed in 1.21.1

Check your own hosts for these packages with threat-finder (opens in a new tab), our free open-source scanner.

AI-suggested

The only effective mitigation is to upgrade htslib to version 1.21.1, 1.22.2, 1.23.1, or later, where the NULL pointer dereference issue has been fixed. Organizations should audit their environments to identify all instances of samtools and htslib and verify the versions in use. Automated deployment tools can facilitate rapid patching across research clusters and production systems. Since no workaround exists, blocking or filtering CRAM files from untrusted sources may reduce exposure but is not a substitute for patching. Implementing input validation and sandboxing bioinformatics processing pipelines can limit the impact of crashes. Monitoring for abnormal application crashes or denial-of-service symptoms during CRAM file processing can help detect exploitation attempts. Finally, maintaining an inventory of bioinformatics tools and dependencies and integrating vulnerability management into research IT operations will improve resilience against similar issues.

Description

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `CONST`, `XPACK` and `XRLE` encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. 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.

Impact

The primary impact of CVE-2026-31964 is denial of service caused by application crashes when processing specially crafted CRAM files with omitted sequence or quality data using vulnerable htslib versions. This can disrupt bioinformatics workflows, delay genomic data analysis, and potentially halt critical research or clinical diagnostics relying on samtools. While the vulnerability does not directly expose sensitive data or allow code execution, the availability impact can be significant in environments where continuous processing of large genomic datasets is essential. Organizations relying on automated pipelines for DNA sequence alignment and analysis may experience interruptions, leading to operational delays and increased costs. Additionally, if exploited in a targeted manner, attackers could disrupt services in research or healthcare settings, impacting patient care or scientific progress. The lack of authentication or user interaction requirements increases the risk of remote exploitation by submitting malicious CRAM files to vulnerable systems.

Summary

CVE-2026-31964 is a vulnerability in the htslib library, a core component of samtools widely used for reading and writing bioinformatics file formats, including CRAM, which compresses DNA sequence alignment data. The CRAM format allows omission of sequence and quality data in certain records to save space, but these records must still be processed carefully. The vulnerability arises because the CONST, XPACK, and XRLE encodings in htslib did not correctly implement the interface to handle these omitted data records, leading to attempts to write to a NULL pointer during decoding. This NULL pointer dereference results in a program crash, causing a denial-of-service condition. The issue affects htslib versions before 1.21.1, versions from 1.22 up to but not including 1.22.2, and version 1.23.1. The vulnerability requires no authentication or user interaction and can be triggered remotely by processing crafted CRAM files. The CVSS 4.0 base score of 6.9 reflects the medium severity, with network attack vector, low complexity, no privileges required, and no user interaction needed. The impact is limited to availability due to crashes, with no direct confidentiality or integrity compromise. This vulnerability is particularly relevant to organizations processing genomic data using samtools and htslib, including research labs, healthcare institutions, and biotech firms.

CWE-476NULL Pointer Dereference (opens in a new tab)
Base weaknessLikelihood of exploit: MediumCWE Top 25 (2025): #13OWASP Top 10 A10:2025: Mishandling of Exceptional Conditions (opens in a new tab)
The product dereferences a pointer that it expects to be valid but is NULL.
Implementation
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.
Requirements
Select a programming language that is not susceptible to these issues.
Implementation
Check the results of all functions that return a value and verify that the value is non-null before acting upon it.
OWASP Cheat Sheets
Logging (opens in a new tab)
Error Handling (opens in a new tab)
OWASP ASVS 4.0.3
V11.1.7 (opens in a new tab)
From MITRE CWE, MITRE CAPEC and OWASP (Top 10, OpenCRE).

References

Community reviews

Loading reviews…

Exploitation evidence

What to do

Affected software

Description

AI analysisMachine-generated, updated 18 Mar 2026, 18:58 UTC

WeaknessesCWE-476

Technical details

References

Community reviews

Related threats