diff --git a/Dockerfile b/Dockerfile
index 49733ff6..15a38f80 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -35,7 +35,7 @@ RUN cd /opt/gridss/src/main/c/gridsstools/htslib && \
 	cp gridsstools /opt/gridss/
 
 # compile GRIDSS Java code
-FROM maven:3.6.3-jdk-8 AS gridss_builder_java
+FROM maven:3.8.4-jdk-11 AS gridss_builder_java
 RUN mkdir /opt/gridss/
 WORKDIR /opt/gridss/
 # Download maven dependencies first so docker can cache them
diff --git a/pom.xml b/pom.xml
index ff3c1c3a..5402646d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,222 +1,221 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<groupId>au.edu.wehi</groupId>
-	<artifactId>gridss</artifactId>
-	<packaging>jar</packaging>
-	<version>${revision}-gridss</version>
-	<name>gridss</name>
-	<url>https://github.com/PapenfussLab/gridss</url>
-	<properties>
-		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-		<revision>0.0.1-SNAPSHOT</revision>
-	</properties>
-	<licenses>
-		<license>
-			<name>GNU General Public License (GPL)</name>
-			<url>http://www.gnu.org/licenses/gpl.txt</url>
-		</license>
-	</licenses>
-	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-jar-plugin</artifactId>
-				<version>3.2.0</version>
-				<configuration>
-					<archive>
-						<manifest>
-							<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
-							<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
-						</manifest>
-						<manifestEntries>
-							<Multi-Release>true</Multi-Release>
-						</manifestEntries>
-					</archive>
-				</configuration>
-			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-compiler-plugin</artifactId>
-				<version>3.9.0</version>
-				<configuration>
-					<!--
-					<source>1.8</source>
-					<target>1.8</target>
-					-->
-					<release>8</release>
-					<multiReleaseOutput>true</multiReleaseOutput>
-				</configuration>
-			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-shade-plugin</artifactId>
-				<version>3.2.4</version>
-				<executions>
-					<execution>
-						<phase>package</phase>
-						<goals>
-							<goal>shade</goal>
-						</goals>
-						<configuration>
-							<finalName>${project.artifactId}-${project.version}-jar-with-dependencies</finalName>
-							<transformers>
-								<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
-									<mainClass>>gridss.CallVariants</mainClass>
-								</transformer>
-							</transformers>
-							<artifactSet>
-								<excludes>
-								</excludes>
-							</artifactSet>
-						</configuration>
-					</execution>
-				</executions>
-			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-surefire-plugin</artifactId>
-				<version>2.19.1</version>
-				<configuration>
-					<excludedGroups>au.edu.wehi.idsv.Hg19Tests,au.edu.wehi.idsv.Hg38Tests,au.edu.wehi.idsv.EColiTests,au.edu.wehi.idsv.alignment.ExternalAlignerTests,au.edu.wehi.idsv.alignment.JniAlignerTests</excludedGroups>
-					<argLine>-Xmx4g</argLine>
-				</configuration>
-			</plugin>
-			<plugin>
-				<groupId>org.jacoco</groupId>
-				<artifactId>jacoco-maven-plugin</artifactId>
-				<version>0.7.7.201606060606</version>
-				<executions>
-					<execution>
-						<id>default-prepare-agent</id>
-						<goals>
-							<goal>prepare-agent</goal>
-						</goals>
-					</execution>
-					<execution>
-						<id>default-report</id>
-						<phase>prepare-package</phase>
-						<goals>
-							<goal>report</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
-			<plugin>
-				<groupId>org.eluder.coveralls</groupId>
-				<artifactId>coveralls-maven-plugin</artifactId>
-				<version>4.2.0</version>
-			</plugin>
-		</plugins>
-	</build>
-	<repositories>
-		<repository>
-			<id>project.local</id>
-			<name>project</name>
-			<url>file:${project.basedir}/repo</url>
-		</repository>
-	</repositories>
-	<dependencies>
-		<dependency>
-			<groupId>jaligner</groupId>
-			<artifactId>jaligner</artifactId>
-			<version>1.0</version>
-		</dependency>
-		<dependency>
-			<groupId>ssw</groupId>
-			<artifactId>ssw</artifactId>
-			<version>1.0</version>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-			<version>4.13.1</version>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>com.google.guava</groupId>
-			<artifactId>guava</artifactId>
-			<version>30.0-jre</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-lang3</artifactId>
-			<version>3.10</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-math3</artifactId>
-			<version>3.6.1</version>
-		</dependency>
-		<dependency>
-			<groupId>commons-io</groupId>
-			<artifactId>commons-io</artifactId>
-			<version>2.7</version>
-		</dependency>
-		<dependency>
-			<groupId>commons-configuration</groupId>
-			<artifactId>commons-configuration</artifactId>
-			<version>1.10</version>
-		</dependency>
-		<dependency>
-			<groupId>it.uniroma1.dis.wsngroup.gexf4j</groupId>
-			<artifactId>gexf4j</artifactId>
-			<version>1.0.0</version>
-		</dependency>
-		<dependency>
-			<groupId>it.unimi.dsi</groupId>
-			<artifactId>fastutil</artifactId>
-			<version>8.3.1</version>
-		</dependency>
-		<dependency>
-			<groupId>net.sf.trove4j</groupId>
-			<artifactId>trove4j</artifactId>
-			<version>3.0.3</version>
-		</dependency>
-		<dependency>
-			<groupId>com.github.samtools</groupId>
-			<artifactId>htsjdk</artifactId>
-			<version>2.23.0</version>
-		</dependency>
-		<dependency>
-			<groupId>com.github.broadinstitute</groupId>
-			<artifactId>picard</artifactId>
-			<version>2.23.2</version>
-		</dependency>
-		<dependency>
-			<groupId>org.broadinstitute</groupId>
-			<artifactId>barclay</artifactId>
-			<version>3.0.0</version>
-		</dependency>
-		<dependency>
-			<groupId>org.broadinstitute</groupId>
-			<artifactId>gatk-bwamem-jni</artifactId>
-			<version>1.0.5</version>
-		</dependency>
-		<dependency>
-			<groupId>org.broadinstitute</groupId>
-			<artifactId>gatk-minimap2-jni</artifactId>
-			<version>1.0.2</version>
-		</dependency>
-		<dependency>
-			<groupId>com.intel.gkl</groupId>
-			<artifactId>gkl</artifactId>
-			<version>0.8.6</version>
-		</dependency>
-	</dependencies>
-	<dependencyManagement>
-		<dependencies>
-			<dependency>
-				<groupId>org.apache.logging.log4j</groupId>
-				<artifactId>log4j-bom</artifactId>
-				<version>2.17.1</version>
-				<scope>import</scope>
-				<type>pom</type>
-			</dependency>
-		</dependencies>
-	</dependencyManagement>
-	<scm>
-		<developerConnection>Daniel Cameron</developerConnection>
-		<url>https://github.com/PapenfussLab/gridss</url>
-	</scm>
-</project>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<groupId>au.edu.wehi</groupId>
+	<artifactId>gridss</artifactId>
+	<packaging>jar</packaging>
+	<version>${revision}-gridss</version>
+	<name>gridss</name>
+	<url>https://github.com/PapenfussLab/gridss</url>
+	<properties>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+		<revision>0.0.1-SNAPSHOT</revision>
+	</properties>
+	<licenses>
+		<license>
+			<name>GNU General Public License (GPL)</name>
+			<url>http://www.gnu.org/licenses/gpl.txt</url>
+		</license>
+	</licenses>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-jar-plugin</artifactId>
+				<version>3.2.0</version>
+				<configuration>
+					<archive>
+						<manifest>
+							<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+							<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
+						</manifest>
+						<manifestEntries>
+							<Multi-Release>true</Multi-Release>
+						</manifestEntries>
+					</archive>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>3.9.0</version>
+				<configuration>
+					<source>1.8</source>
+					<target>1.8</target>
+					<release>8</release>
+					<!-- don't have multi-release output in the java8 configuration because we want it to be in the default location at the jar root -->
+					<!--<multiReleaseOutput>true</multiReleaseOutput>-->
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-shade-plugin</artifactId>
+				<version>3.2.4</version>
+				<executions>
+					<execution>
+						<phase>package</phase>
+						<goals>
+							<goal>shade</goal>
+						</goals>
+						<configuration>
+							<finalName>${project.artifactId}-${project.version}-jar-with-dependencies</finalName>
+							<transformers>
+								<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+									<mainClass>>gridss.CallVariants</mainClass>
+								</transformer>
+							</transformers>
+							<artifactSet>
+								<excludes>
+								</excludes>
+							</artifactSet>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<version>2.19.1</version>
+				<configuration>
+					<excludedGroups>au.edu.wehi.idsv.Hg19Tests,au.edu.wehi.idsv.Hg38Tests,au.edu.wehi.idsv.EColiTests,au.edu.wehi.idsv.alignment.ExternalAlignerTests,au.edu.wehi.idsv.alignment.JniAlignerTests</excludedGroups>
+					<argLine>-Xmx4g</argLine>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.jacoco</groupId>
+				<artifactId>jacoco-maven-plugin</artifactId>
+				<version>0.7.7.201606060606</version>
+				<executions>
+					<execution>
+						<id>default-prepare-agent</id>
+						<goals>
+							<goal>prepare-agent</goal>
+						</goals>
+					</execution>
+					<execution>
+						<id>default-report</id>
+						<phase>prepare-package</phase>
+						<goals>
+							<goal>report</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.eluder.coveralls</groupId>
+				<artifactId>coveralls-maven-plugin</artifactId>
+				<version>4.2.0</version>
+			</plugin>
+		</plugins>
+	</build>
+	<repositories>
+		<repository>
+			<id>project.local</id>
+			<name>project</name>
+			<url>file:${project.basedir}/repo</url>
+		</repository>
+	</repositories>
+	<dependencies>
+		<dependency>
+			<groupId>jaligner</groupId>
+			<artifactId>jaligner</artifactId>
+			<version>1.0</version>
+		</dependency>
+		<dependency>
+			<groupId>ssw</groupId>
+			<artifactId>ssw</artifactId>
+			<version>1.0</version>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.13.1</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+			<version>30.0-jre</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-lang3</artifactId>
+			<version>3.10</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-math3</artifactId>
+			<version>3.6.1</version>
+		</dependency>
+		<dependency>
+			<groupId>commons-io</groupId>
+			<artifactId>commons-io</artifactId>
+			<version>2.7</version>
+		</dependency>
+		<dependency>
+			<groupId>commons-configuration</groupId>
+			<artifactId>commons-configuration</artifactId>
+			<version>1.10</version>
+		</dependency>
+		<dependency>
+			<groupId>it.uniroma1.dis.wsngroup.gexf4j</groupId>
+			<artifactId>gexf4j</artifactId>
+			<version>1.0.0</version>
+		</dependency>
+		<dependency>
+			<groupId>it.unimi.dsi</groupId>
+			<artifactId>fastutil</artifactId>
+			<version>8.3.1</version>
+		</dependency>
+		<dependency>
+			<groupId>net.sf.trove4j</groupId>
+			<artifactId>trove4j</artifactId>
+			<version>3.0.3</version>
+		</dependency>
+		<dependency>
+			<groupId>com.github.samtools</groupId>
+			<artifactId>htsjdk</artifactId>
+			<version>2.23.0</version>
+		</dependency>
+		<dependency>
+			<groupId>com.github.broadinstitute</groupId>
+			<artifactId>picard</artifactId>
+			<version>2.23.2</version>
+		</dependency>
+		<dependency>
+			<groupId>org.broadinstitute</groupId>
+			<artifactId>barclay</artifactId>
+			<version>3.0.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.broadinstitute</groupId>
+			<artifactId>gatk-bwamem-jni</artifactId>
+			<version>1.0.5</version>
+		</dependency>
+		<dependency>
+			<groupId>org.broadinstitute</groupId>
+			<artifactId>gatk-minimap2-jni</artifactId>
+			<version>1.0.2</version>
+		</dependency>
+		<dependency>
+			<groupId>com.intel.gkl</groupId>
+			<artifactId>gkl</artifactId>
+			<version>0.8.6</version>
+		</dependency>
+	</dependencies>
+	<dependencyManagement>
+		<dependencies>
+			<dependency>
+				<groupId>org.apache.logging.log4j</groupId>
+				<artifactId>log4j-bom</artifactId>
+				<version>2.17.1</version>
+				<scope>import</scope>
+				<type>pom</type>
+			</dependency>
+		</dependencies>
+	</dependencyManagement>
+	<scm>
+		<developerConnection>Daniel Cameron</developerConnection>
+		<url>https://github.com/PapenfussLab/gridss</url>
+	</scm>
+</project>