diff --git a/pom.xml b/pom.xml
index 2c30ec36..f13a72eb 100644
--- a/pom.xml
+++ b/pom.xml
@@ -26,7 +26,7 @@
 		<dependency>
 			<groupId>com.github.samtools</groupId>
 			<artifactId>htsjdk</artifactId>
-			<version>2.12.0</version>
+			<version>3.0.1</version>
 		</dependency>
 		<dependency>
 			<groupId>junit</groupId>