diff --git a/pom.xml b/pom.xml
index ed2d8ebed..37c49ea80 100644
--- a/pom.xml
+++ b/pom.xml
@@ -27,7 +27,7 @@
      <!-- Edit the following line to configure the Hadoop (HDFS) version. -->
     <hadoop.version>3.2.1</hadoop.version>
     <hadoop-bam.version>7.9.2</hadoop-bam.version>
-    <htsjdk.version>2.19.0</htsjdk.version>
+    <htsjdk.version>3.0.1</htsjdk.version>
     <parquet.version>1.10.1</parquet.version>
     <scala.version>2.12.10</scala.version>
     <scala.version.prefix>2.12</scala.version.prefix>