diff --git a/build.gradle b/build.gradle
index d466ff63f46..ca4658fd0de 100644
--- a/build.gradle
+++ b/build.gradle
@@ -60,7 +60,7 @@ repositories {
     mavenLocal()
 }
 
-final htsjdkVersion = System.getProperty('htsjdk.version','2.24.1')
+final htsjdkVersion = System.getProperty('htsjdk.version','3.0.0')
 final picardVersion = System.getProperty('picard.version','2.27.1')
 final barclayVersion = System.getProperty('barclay.version','4.0.2')
 final sparkVersion = System.getProperty('spark.version', '2.4.5')