diff --git a/build.gradle b/build.gradle
index c160678241..10b66ed405 100644
--- a/build.gradle
+++ b/build.gradle
@@ -59,7 +59,7 @@ def ensureBuildPrerequisites(buildPrerequisitesMessage) {
 
 ensureBuildPrerequisites(buildPrerequisitesMessage)
 
-final htsjdkVersion = System.getProperty('htsjdk.version', '4.1.1')
+final htsjdkVersion = System.getProperty('htsjdk.version', '4.1.3')
 final log4jVersion = System.getProperty('log4j.version', '2.20.0')
 
 dependencies {