Samtools vulnerabilities
We track 13 vulnerabilities in Samtools products across 3 products. 13 are rated high or critical, and none are known to be exploited. The most recent was published on March 18, 2026.
Latest Samtools vulnerabilities
- 7.5 High severity
samtools: NULL Pointer Dereference
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_head
- 9.8 Critical severity
samtools: Use After Free
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 referenc
- 8.1 High severity
htslib: Stack-based Buffer Overflow
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_LEN` method, the
- 8.1 High severity
htslib: Heap-based Buffer Overflow
HTSlib is a library for reading and writing bioinformatics file formats. GZI files are used to index block-compressed GZIP [BGZF] files. In the GZI loading function, `bgzf_index_load_hfile()`, it was possible to trigger an integer overflow, leading to an under
- 8.1 High severity
htslib: Heap-based Buffer Overflow
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_STOP` method, an
- 8.1 High severity
htslib: Stack-based Buffer Overflow
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. For the `VARINT` and `CONST` encodings, incomplete validation of
- 9.1 Critical severity
htslib: Out-of-bounds Read
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the `cram_decode_slice()` function called while reading CRAM records, the value of the mate reference id field was
- 9.1 Critical severity
htslib: Out-of-bounds Read
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 s
- 8.2 High severity
htslib: Out-of-bounds Read
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the `cram_decode_slice()` function called while reading CRAM records, validation of the reference id field occurre
- 7.5 High severity
htslib: NULL Pointer Dereference
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. While most alignment records store DNA sequence and quality valu
- 8.1 High severity
htslib: Heap-based Buffer Overflow
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 s
- 8.8 High severity
htslib: Heap-based Buffer Overflow
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in
- 7.8 High severity
com.github.samtools:htsjdk: Exposure of Resource to Wrong Sphere
The package com.github.samtools:htsjdk before 3.0.1 are vulnerable to Creation of Temporary File in Directory with Insecure Permissions due to the createTempDir() function in util/IOUtil.java not checking for the existence of the temporary directory before att