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. Impact ------ 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. Severity -------- Moderate CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N Patches ------- This bug is fixed in versions 1.21.1 and 1.22 Workarounds ----------- There is no workaround for this issue. References ---------- https://github.com/samtools/samtools/security/advisories/GHSA-72c8-4jf3-f27p https://www.cve.org/CVERecord?id=CVE-2026-31972 -- The SAMtools team https://www.htslib.org/ https://www.sanger.ac.uk/ ---------------------------------------------------------------------- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA.
