diff --git a/build.gradle b/build.gradle
index 10b66ed405..625310566a 100644
--- a/build.gradle
+++ b/build.gradle
@@ -59,7 +59,7 @@ def ensureBuildPrerequisites(buildPrerequisitesMessage) {
 
 ensureBuildPrerequisites(buildPrerequisitesMessage)
 
-final htsjdkVersion = System.getProperty('htsjdk.version', '4.1.3')
+final htsjdkVersion = System.getProperty('htsjdk.version', '4.1.0-6-g50fec4b-SNAPSHOT')
 final log4jVersion = System.getProperty('log4j.version', '2.20.0')
 
 dependencies {