diff --git a/pom.xml b/pom.xml
index 6c1e339ac..dfd76b804 100644
--- a/pom.xml
+++ b/pom.xml
@@ -28,7 +28,7 @@
     <bdg-formats.version>1.0.1</bdg-formats.version>
     <bdg-utils.version>1.0</bdg-utils.version>
     <grizzled-slf4j.version>1.3.4</grizzled-slf4j.version>
-    <htsjdk.version>2.19.0</htsjdk.version>
+    <htsjdk.version>3.0.1</htsjdk.version>
     <scoverage.plugin.version>1.1.1</scoverage.plugin.version>
   </properties>