VulnerabilityPublished 18 Mar 2026

CVE-2026-31963: samtools htslib · Heap-based Buffer Overflow

Affects samtools htslibSource CVE Database V5

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Not known to be exploited · CVSS 8.8 High : upgrade to 1.22.2 or 1.21.1 soon.

Data as of 31 Oct 2026, 20:20 UTC

CVSS 4.0 base score

8.8High

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

EPSS: 0.3% chance of exploitation in 30 days – higher than 29% 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:H/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: High
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: High: There is a total loss of integrity, or a complete loss of protection. For example, the attacker is able to modify any/all files protected by the vulnerable system. Alternatively, only some files can be modified, but malicious modification would present a direct, serious consequence 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 31 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

Organizations should immediately identify and inventory all instances of samtools and htslib in their environments, especially those processing CRAM files. They must upgrade to fixed versions 1.21.1, 1.22.2, or 1.23.1 or later as soon as possible. For environments where immediate patching is challenging, consider isolating systems that process external or untrusted CRAM files to limit exposure. Implement strict input validation and scanning of bioinformatics data files before processing to detect potentially malformed or malicious CRAM files. Employ runtime protections such as heap memory protection mechanisms (e.g., ASLR, heap canaries) and sandboxing of bioinformatics tools to reduce the impact of exploitation. Monitor systems for unusual crashes or behavior indicative of exploitation attempts. Additionally, maintain up-to-date threat intelligence feeds to detect any emerging exploit activity targeting this vulnerability. Finally, establish secure data handling policies and restrict access to bioinformatics processing environments to trusted personnel and systems.

Description

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by the program. It may be possible to use this to obtain arbitrary code execution. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.

Impact

This vulnerability can have severe consequences for organizations that utilize samtools and htslib for genomic data processing, including research institutions, healthcare providers, pharmaceutical companies, and biotech firms. Exploitation could lead to denial of service through application crashes or, more dangerously, arbitrary code execution, potentially allowing attackers to execute malicious payloads within the context of the vulnerable application. This could compromise sensitive genomic data confidentiality and integrity, disrupt critical bioinformatics workflows, and potentially serve as a foothold for further network intrusion. Given the specialized nature of the software, the impact is concentrated in sectors handling DNA sequencing data but can affect any organization relying on vulnerable versions. The lack of required authentication or user interaction increases the risk, especially in automated pipelines processing untrusted data. The absence of workarounds further elevates the urgency to apply patches promptly to avoid exploitation.

Summary

The vulnerability CVE-2026-31963 affects the htslib library, a core component of samtools widely used for reading and writing bioinformatics file formats such as CRAM, which compresses DNA sequence alignment data by referencing external sequences and encoding differences as features. The issue stems from an out-of-bounds write caused by an off-by-one error during the decoding of CRAM features that extend beyond the actual sequence length. This results in a heap-based buffer overflow where one attacker-controlled byte is written beyond the allocated heap buffer. Such memory corruption can lead to program instability, crashes, or more critically, arbitrary code execution if exploited successfully. The vulnerability requires no privileges or user interaction, making it remotely exploitable simply by opening a maliciously crafted CRAM file. The affected versions are those prior to 1.21.1, between 1.22 and 1.22.2, and version 1.23.1. The developers have released patches in versions 1.21.1, 1.22.2, and 1.23.1 to address this flaw. No alternative mitigations or workarounds are available, emphasizing the need for timely patching. The CVSS 4.0 base score is 8.8, reflecting its high severity due to ease of exploitation and potential impact on confidentiality and integrity of systems processing genomic data.

CWE-122Heap-based Buffer Overflow (opens in a new tab)
Variant weaknessLikelihood of exploit: HighCWE Top 25 (2025): #16
The product writes past the end of a buffer that was allocated on the heap.
Pre-design: Use a language or compiler that performs automatic bounds checking.
Architecture and Design
Use an abstraction library to abstract away risky APIs. Not a complete solution.
Operation · Build and Compilation · Environment Hardening
Use automatic buffer overflow detection mechanisms that are offered by certain compilers or compiler extensions. Examples include: the Microsoft Visual Studio /GS flag, Fedora/Red Hat FORTIFY_SOURCE GCC flag, StackGuard, and ProPolice, which provide various mechanisms including canary-based detection and range/index…
OWASP Cheat Sheets
XML Security (opens in a new tab)
Mass Assignment (opens in a new tab)
OWASP ASVS 4.0.3
V13.3.1 (opens in a new tab)
V5.1.4 (opens in a new tab)
V5.1.3 (opens in a new tab)
Attack patterns
Forced Integer Overflow (opens in a new tab)
From MITRE CWE, MITRE CAPEC and OWASP (Top 10, OpenCRE).
CWE-129Improper Validation of Array Index (opens in a new tab)
Variant weaknessLikelihood of exploit: HighOWASP Top 10 A05:2025: Injection (opens in a new tab)
The product uses untrusted input when calculating or using an array index, but the product does not validate or incorrectly validates the index to ensure the index references a valid position within the array.
Architecture and Design · Input Validation
Use an input validation framework such as Struts or the OWASP ESAPI Validation API. Note that using a framework does not automatically address all input validation problems; be mindful of weaknesses that could arise from misusing the framework itself (CWE-1173).
Architecture and Design
For any security checks that are performed on the client side, ensure that these checks are duplicated on the server side, in order to avoid CWE-602. Attackers can bypass the client-side checks by modifying values after the checks have been performed, or by changing the client to remove the client-side checks…
Requirements · Language Selection
Use a language that does not allow this weakness to occur or provides constructs that make this weakness easier to avoid.
OWASP Cheat Sheets
XML Security (opens in a new tab)
Mass Assignment (opens in a new tab)
Injection Prevention (opens in a new tab)
SQL Injection Prevention (opens in a new tab)
Injection Prevention in Java (opens in a new tab)
OWASP ASVS 4.0.3
V13.3.1 (opens in a new tab)
V5.1.4 (opens in a new tab)
V5.1.3 (opens in a new tab)
Attack patterns
Overflow Buffers (opens in a new tab)
From MITRE CWE, MITRE CAPEC and OWASP (Top 10, OpenCRE).
CWE-787Out-of-bounds Write (opens in a new tab)
Base weaknessLikelihood of exploit: HighCWE Top 25 (2025): #5
The product writes data past the end, or before the beginning, of the intended buffer.
Requirements · Language Selection
Use a language that does not allow this weakness to occur or provides constructs that make this weakness easier to avoid.
Architecture and Design · Libraries or Frameworks
Use a vetted library or framework that does not allow this weakness to occur or provides constructs that make this weakness easier to avoid.
Operation · Build and Compilation · Environment Hardening
Use automatic buffer overflow detection mechanisms that are offered by certain compilers or compiler extensions. Examples include: the Microsoft Visual Studio /GS flag, Fedora/Red Hat FORTIFY_SOURCE GCC flag, StackGuard, and ProPolice, which provide various mechanisms including canary-based detection and range/index…
OWASP Cheat Sheets
XML Security (opens in a new tab)
Mass Assignment (opens in a new tab)
OWASP ASVS 4.0.3
V13.3.1 (opens in a new tab)
V5.1.4 (opens in a new tab)
V5.1.3 (opens in a new tab)
From MITRE CWE, MITRE CAPEC and OWASP (Top 10, OpenCRE).

References

Community reviews

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Exploitation evidence

What to do

Affected software

Description

AI analysisMachine-generated, updated 18 Mar 2026, 18:57 UTC

WeaknessesCWE-122, CWE-129, CWE-787

Technical details

References

Community reviews

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