diff --git a/NanostreamDataflowMain/pipeline/pom.xml b/NanostreamDataflowMain/pipeline/pom.xml
index 8fa121e5..04bba982 100644
--- a/NanostreamDataflowMain/pipeline/pom.xml
+++ b/NanostreamDataflowMain/pipeline/pom.xml
@@ -98,7 +98,7 @@
         <dependency>
             <groupId>com.github.samtools</groupId>
             <artifactId>htsjdk</artifactId>
-            <version>2.10.1</version>
+            <version>3.0.1</version>
         </dependency>
         <dependency>
             <groupId>coin</groupId>