diff --git a/pom.xml b/pom.xml
index b0b89d08..7dc6d608 100644
--- a/pom.xml
+++ b/pom.xml
@@ -154,7 +154,7 @@
     <dependency>
       <groupId>com.github.samtools</groupId>
       <artifactId>htsjdk</artifactId>
-      <version>2.21.0</version>
+      <version>3.0.1</version>
     </dependency>
     <dependency>
       <groupId>joda-time</groupId>