diff --git a/pom.xml b/pom.xml
index e11524d7d..0aadab7a2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -19,7 +19,7 @@
 
 		<java.version>11</java.version>
 		<hadoop.version>2.3.0</hadoop.version>
-		<htsjdk.version>2.13.2</htsjdk.version>
+		<htsjdk.version>3.0.1</htsjdk.version>
 		<kenetre.version>0.12</kenetre.version>
 		<poi.version>4.1.2</poi.version>