CVE-2026-31973: SAMtools is a program for reading, manipulating and writing bioinformatics file formats

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HIGH 7.5REMOTEUPGRADE

CVE-2026-31973 is a high-severity flaw (CVSS 7.5) affecting samtools. Below: why it ranks where it does, which versions are affected, what to do, and the exact commands.

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 prog

Why this priority

High severity
Remotely exploitable, no login, no user action

A fixed release or distro patch exists.

Risk facts

CVSS score	7.5 (High)
Attack vector	Network (remote)
Attack complexity	Low
Privileges needed	None
User interaction	None
EPSS exploit chance	0.5% (top 54%)
CISA exploited list	No
Weakness	CWE-476
Published	2026-03-18
Last modified	2026-06-17

Publisher (CNA): GitHub, Inc. · Vendor: samtools

Last updated 2026-06-17 · Sources: CVE Program, NVD, CISA KEV, EPSS and vendor advisories · How we score

Am I affected?

Timeline

2026-03-18 21:16 UTCPublished CVE record published
2026-06-17 10:34 UTCUpdated Record last modified

samtools samtools UPGRADE

Affected: >= 1.17 and <= 1.21.1 · >= 1.22 and < 1.22.2 · 1.23

Fixed in: 1.22.2

Safe to downgrade to: a release before 1.17

1. Check installed version

apt-cache policy samtools || rpm -q samtools || samtools --version

2. UPGRADE to 1.22.2 (Debian / Ubuntu)

sudo apt update && sudo apt install --only-upgrade samtools

2. UPGRADE (RHEL / Amazon Linux / Fedora)

sudo dnf upgrade samtools

Note

Distros often backport fixes without changing the version number. Confirm with the distro advisory or changelog.

3. If no update is available yet, DOWNGRADE to a release before 1.17 (Debian / Ubuntu)

apt-cache madison samtools sudo apt install samtools=<VERSION_BEFORE_1.17> sudo apt-mark hold samtools

3. If no update is available yet, DOWNGRADE (RHEL / Amazon Linux / Fedora)

dnf --showduplicates list samtools sudo dnf downgrade samtools-<VERSION_BEFORE_1.17> sudo dnf versionlock add samtools

Downgrade risk

Downgrading can break dependent software and may reopen older bugs. Read the distro advisory first and test on a non-production host.

After downgrade

Restart the service, and keep the package held until a fixed release ships.

Verify at the official source NVD · CVE Program · Report a problem with this page
Scores and fixes here are computed automatically from those and other public sources. Confirm with the vendor advisory before changing production systems.

Quick answers

How do I fix CVE-2026-31973?

samtools: upgrade to 1.22.2. Exact commands for each OS are on this page.

Is CVE-2026-31973 being exploited?

CVE-2026-31973 is not on the CISA Known Exploited Vulnerabilities list at the time of the last update. Check again, as this can change.

What does CVE-2026-31973 affect?

CVE-2026-31973 affects samtools. Severity is high (CVSS 7.5). 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_dec

How urgent is CVE-2026-31973?

Priority 43/100. High severity; Remotely exploitable, no login, no user action

Related CVEs

CVE-2026-31972 CRITICAL 9.8 UPGRADE SAMtools is a program for reading, manipulating and writing bioinformatics file formats

References

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