diff --git a/pom.xml b/pom.xml
index f6eb9f3a..2f8b91ec 100644
--- a/pom.xml
+++ b/pom.xml
@@ -93,7 +93,7 @@
         <dependency>
             <groupId>com.github.samtools</groupId>
             <artifactId>htsjdk</artifactId>
-            <version>2.14.3</version>
+            <version>3.0.1</version>
         </dependency>
 	<dependency>
 	    <groupId>org.jgrapht</groupId>