What is the CVSS score of CVE-2026-31963?

CVE-2026-31963 has a CVSS 4.0 base score of 8.8 (High). CVSS vector: 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. EPSS exploitation probability: 0.1%.

Which versions of Htslib are affected by CVE-2026-31963?

Organizations using HTSlib face significant risk from CVE-2026-31963, a heap-based buffer overflow vulnerability rated CVSS 8.8.. A patch is available.

How to fix or mitigate CVE-2026-31963?

Within 7 days: Identify all affected systems and apply vendor patches promptly. If patching is delayed, consider network segmentation to limit exposure.

Htslib CVE-2026-31963

EUVD-2026-12930 HIGH

Heap-based Buffer Overflow (CWE-122)

2026-03-18 GitHub_M

Buffer Overflow Heap Overflow Denial Of Service RCE Debian Htslib Red Hat

8.8

CVSS 4.0 · GitHub Advisory

Severity by source

GitHub Advisory PRIMARY

8.8 HIGH

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

Red Hat

7.3 HIGH

qualitative

Primary rating from GitHub Advisory.

CVSS VectorGitHub Advisory

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

Privileges Required

None

User Interaction

None

Lifecycle Timeline

Patch released

Mar 31, 2026 - 21:13 nvd

Patch available

EUVD ID Assigned

Mar 18, 2026 - 18:45 euvd

EUVD-2026-12930

Analysis Generated

Mar 18, 2026 - 18:45 vuln.today

CVE Published

Mar 18, 2026 - 18:22 nvd

HIGH 8.8

DescriptionGitHub Advisory

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.

AnalysisAI

HTSlib contains a heap buffer overflow vulnerability in its CRAM decoder caused by an out-by-one error when validating feature boundaries. When a user opens a maliciously crafted CRAM file, an attacker can write one controlled byte beyond the end of a heap buffer, potentially causing application crashes, data corruption, or arbitrary code execution. Versions 1.23.1, 1.22.2, and 1.21.1 include fixes, and patches are available via the official GitHub repository.

Technical ContextAI

HTSlib (samtools:htslib) is a widely-used C library for reading and writing bioinformatics data formats, including CRAM—a reference-based compression format for DNA sequence alignment data. CRAM reduces file size by storing only differences (features) relative to external reference sequences rather than full sequence data. The vulnerability stems from a CWE-122 (Heap-based Buffer Overflow) condition in the feature decoding logic: when HTSlib processes CRAM feature records, it performs a boundary check to ensure features do not extend beyond the sequence extent. An off-by-one error in this test allows a single attacker-controlled byte to be written one position past the allocated heap buffer's end. The affected CPE is cpe:2.3:a:samtools:htslib:*:*:*:*:*:*:*:* for versions prior to the patched releases.

RemediationAI

Immediately upgrade HTSlib to version 1.23.1, 1.22.2 (for the 1.22.x branch), or 1.21.1 (for the 1.21.x branch) or later. The patch is available via the official GitHub repository at https://github.com/samtools/htslib/commit/8bcc9907be0f945ddc31796d64f078fa05456acd. There is no documented workaround for this vulnerability; patching is the only mitigation. Organizations unable to patch immediately should restrict access to CRAM file processing infrastructure, validate CRAM file sources before processing, and implement application sandboxing or containerization to limit the impact of potential code execution. Automated dependency scanning should be configured to detect unpatched HTSlib versions in bioinformatics environments.