`CVE-2022-21126` samtools htsjdk

Affected software	samtools htsjdk
Severity	7.8 High CVSS 3.1 2 scores
Fixed in	`3.0.1`
Weakness	CWE-668
Published	29 Nov 2022
Updated	17 Jun 2026

Description

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 attempting to create it.

Exploitation status

Proof of concept only

A proof of concept exists, but no reviewed exploit catalogue lists this CVE.

CISA KEV not listed
VulnCheck KEV not listed
CISA Vulnrichment exploitation: poc CISA recorded that an exploit has been demonstrated. Automatable: no, technical impact: partial.
Indexed PoC none indexed
EPSS 0.75% chance in 30 days

Waratek protection

No exploit published

Within Waratek scope. In the sources we check, nobody has published exploit code for this CVE or reported it being exploited.

A public code fix exists: samtools/htsjdk 4a4024a.

Protection none
Action unverified
Review automated Upstream data
Record active

Decided by	Exploit code for this candidate, published in a reviewed catalogue or a GitHub repository with 5 or more stars, or in use per CISA or VulnCheck; not only a CISA verdict, a forecast, or nothing at all
Finding	This CVE is not listed in CISA KEV or VulnCheck KEV, CISA Vulnrichment records no active exploitation, no reviewed exploit catalogue carries an entry for it, and no GitHub PoC repository for it has 5 or more stars. Nobody has published exploit code worth tracing, so it is not a candidate for a rule ahead of the ones where somebody has; an upstream fix path does exist, so the remediation half of the candidacy still holds. This is a statement about what has been published, not about whether the defect is reachable or serious.
Candidate fix	https://github.com/samtools/htsjdk/commit/4a4024a97ee3e87096df6ad9b22c8260bd527772 : a commit: the change itself

Decided by

Exploit code for this candidate, published in a reviewed catalogue or a GitHub repository with 5 or more stars, or in use per CISA or VulnCheck; not only a CISA verdict, a forecast, or nothing at all

Finding

This CVE is not listed in CISA KEV or VulnCheck KEV, CISA Vulnrichment records no active exploitation, no reviewed exploit catalogue carries an entry for it, and no GitHub PoC repository for it has 5 or more stars. Nobody has published exploit code worth tracing, so it is not a candidate for a rule ahead of the ones where somebody has; an upstream fix path does exist, so the remediation half of the candidacy still holds. This is a statement about what has been published, not about whether the defect is reachable or serious.

Candidate fix

https://github.com/samtools/htsjdk/commit/4a4024a97ee3e87096df6ad9b22c8260bd527772 : a commit: the change itself

CVSS

7.8 HIGH v3.1 CVSS:3.1/AV:L/AC:L/PR:L/UI:N/S:U/C:H/I:H/A:H 2 metrics

We show the highest score from the newest CVSS version. Scores from different versions can't be compared, and the first score listed is sometimes a 0.0 placeholder.

Version Score Band Vector Assigner Type

CVSS 3.1 7.8 HIGH CVSS:3.1/AV:L/AC:L/PR:L/UI:N/S:U/C:H/I:H/A:H NVD Primary published

CVSS 3.1 7.3 HIGH CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:L/I:L/A:L report@snyk.io Secondary

Version	Score	Band	Vector	Assigner	Type
CVSS 3.1	7.8	HIGH	`CVSS:3.1/AV:L/AC:L/PR:L/UI:N/S:U/C:H/I:H/A:H`	NVD	Primary	published
CVSS 3.1	7.3	HIGH	`CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:L/I:L/A:L`	report@snyk.io	Secondary

Affected software and releases

Maven packages

Affected and fixed versions, from OSV.dev

Package Introduced Fixed Last affected

com.github.samtools:htsjdk 0 3.0.1 unbounded

Package	Introduced	Fixed	Last affected
`com.github.samtools:htsjdk`	0	`3.0.1`	unbounded

Products and versions

2 products, 2 version entries

Source	Vendor	Product	Scheme	Affected versions
osv	com.github.samtools	htsjdk	generic	＜ 3.0.1
nvd	samtools	htsjdk	generic	＜ 3.0.1

Source

Vendor

Product

Scheme

Affected versions

osv

com.github.samtools

htsjdk

generic

＜ 3.0.1

nvd

samtools

htsjdk

generic

＜ 3.0.1

References

URL	Tags
https://github.com/samtools/htsjdk/commit/4a4024a97ee3e87096df6ad9b22c8260bd527772	commit
https://github.com/samtools/htsjdk/pull/1617	WEB
https://github.com/samtools/htsjdk	PACKAGE
https://security.snyk.io/vuln/SNYK-JAVA-COMGITHUBSAMTOOLS-3149901	WEB

URL

Timeline

Published	2022-11-29	By the CVE Program.
NVD record modified	2026-06-17	NVD's own last-modified date for this record.

Published

2022-11-29

By the CVE Program.

NVD record modified

2026-06-17

NVD's own last-modified date for this record.

How VRT decided (17 of 24 rules ran)

17 of 24 rules ran. The rest didn't run because an earlier rule had already settled the CVE.

# Rule Outcome Status Detail

identity: Does this identifier describe a vulnerability at all? the first rule that matches decides

1 rejected no match CVE Program withdrawal of this identifier

scope: Is it a vulnerability Waratek protects? the first rule that matches decides

2 armr-patch-file no match An ARMR patch file on disk for this CVE

3 armr-secure-rule-file no match An ARMR security-rule template on disk for this CVE

4 manual-classification no match A researcher's recorded decision for this specific CVE

5 manual classification no match Manual classification of this CVE in the legacy dataset

6 non-java-upstream no match A root cause in non-Java code: an OS kernel, a C library, or a bundled runtime

7 oracle-component no match The defect being in a component of a tracked product the agent does not reach: JavaFX, the Java SE installer, the JInitiator browser plug-in, the native WebLogic proxy plug-in, or a native part of Oracle Application Server or Collaboration Suite (HTTP Server, Web Cache, Internet Directory, mail and calendar servers). Oracle gives these no CPE of their own and names them only in the description.

8 java-client-side no match Oracle's own risk-matrix note saying the CVE is reached only through untrusted code in the Java sandbox (applets, Web Start) or only through a client installation of Java, so a server running its own trusted code is not exposed

9 osv-maven matched In scope Maven packages: com.github.samtools:htsjdk

10 cna-maven-package not reached An affected Maven artifact named by the CNA itself

11 known-cpe-product not reached An NVD CPE naming a product ARMR tracks

12 cna-cpe-product not reached A CPE the CNA published naming a tracked product. Oracle publishes these on advisory day, months before NVD.

13 oracle-advisory-family not reached A tracked product family named in Oracle's own risk matrix. CPE cannot carry a suite name, only a module.

14 cna-named-product not reached A tracked product named in words by the CVE's own CNA, on a record with no CPE yet. Apache and Eclipse publish these on advisory day, before NVD adds CPE data.

15 non-deployable-product not reached The only affected product being a sealed appliance image, where Java runs but no -javaagent can be attached

16 unmatched-product not reached No tracked product matched above, and none present at all

disposition: What do we do about one that is? every rule runs

17 patch-hint matched Mitigation candidate References include candidate fix URL (commit tier): https://github.com/samtools/htsjdk/commit/4a4024a97ee3e87096df6ad9b22c8260bd527772

18 open-source-maven skipped The affected package being open source on Maven, so the fix can be read

19 poc-derivable skipped An indexed exploit clearing the evidence bar to reverse-engineer, where there is no source to read

20 no-exploit skipped Nothing to build a rule from yet: no published exploit, no CISA record of exploitation and no source-level change to read

21 secure-rule-match no match A vulnerability class already blocked by an ARMR security rule

22 exploited-no-fix-or-poc skipped Somebody exploiting this CVE (a CISA or VulnCheck KEV listing, or a CISA verdict of active exploitation), with no fix, source code or PoC to build a rule from

23 below-action-threshold no match Severity is HIGH — only MEDIUM/LOW are deprioritized

24 no-exploit-published decided it matched No exploit published No exploit code has been published, and an upstream fix path does exist, so the remediation half of the candidacy still holds.

Products the scope rules checked

The products this CVE's record names, and whether VRT tracks each one. The scope rules decided on these.

Vendor Product Tracked CPE Source

samtools htsjdk not tracked cpe:2.3:a:samtools:htsjdk:*:*:*:*:*:*:*:*

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