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Medium · 6.9 CVE-2026-31972 EUVD-2026-12956

samtools mpileup has use-after-free leading to an invalid read

Published Mar 18, 2026 · Updated Mar 19, 2026 · Assigned by GitHub_M

Description

SAMtools is a program for reading, manipulating and writing bioinformatics file formats. The `mpileup` command outputs DNA sequences that have been aligned against a known reference. On each output line it writes the reference position, optionally the reference DNA base at that position (obtained from a separate file) and all of the DNA bases that aligned to that position. As the output is ordered by position, reference data that is no longer needed is discarded once it has been printed out. Under certain conditions the data could be discarded too early, leading to an attempt to read from a pointer to freed memory. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt to access invalid memory. This bug is fixed in versions 1.21.1 and 1.22. There is no workaround for this issue.

Affected products

VendorProductAffectedFixed
samtools samtools < 1.21.1 —

Fixed in Linux distributions

Distributions backport fixes, so the version that fixes this vulnerability differs per release — upgrade to at least the version shown. From the distributions' security trackers and advisories.

ReleasePackageFixed inAdvisory
Debian 14 samtools 1.22.1-1 —
Debian 13 samtools No fix yet —
Debian 12 samtools No fix yet —
ReleasePackageFixed inAdvisory
Ubuntu 26.10 samtools No fix yet —
Ubuntu 26.04 LTS samtools No fix yet —
Ubuntu 25.10 samtools No fix yet —
Ubuntu 24.04 LTS samtools No fix yet —
Ubuntu 22.04 LTS samtools No fix yet —
Show 4 more (older releases, extended support, other products)
ReleasePackageFixed inAdvisory
Ubuntu 20.04 LTS samtools No fix yet —
Ubuntu 18.04 LTS samtools No fix yet —
Ubuntu 16.04 LTS samtools No fix yet —
Ubuntu 14.04 LTS samtools No fix yet —

References