CVE-2026-31973: Samtools

High severity, CVSS 7.5. EPSS: 0.6% chance of exploitation in the next 30 days.

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 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.

Affected products

• Samtools Samtools: from 1.17, up to and including 1.21.1; from 1.22, before 1.22.2 (fixed in 1.22.2); version 1.23 only

Published 2026-03-18. Last modified 2026-06-17.