gatk
Used in:
components
- OverviewOverview
- VersionsVersions
- DependentsDependents
- DependenciesDependencies
<dependency>
<groupId>org.broadinstitute</groupId>
<artifactId>gatk</artifactId>
<version>4.6.2.0</version>
</dependency><?xml version="1.0" encoding="UTF-8"?>
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<!-- This module was also published with a richer model, Gradle metadata, -->
<!-- which should be used instead. Do not delete the following line which -->
<!-- is to indicate to Gradle or any Gradle module metadata file consumer -->
<!-- that they should prefer consuming it instead. -->
<!-- do_not_remove: published-with-gradle-metadata -->
<modelVersion>4.0.0</modelVersion>
<groupId>org.broadinstitute</groupId>
<artifactId>gatk</artifactId>
<version>4.6.2.0</version>
<name>GATK4</name>
<description>Development on GATK 4</description>
<url>https://github.com/broadinstitute/gatk</url>
<licenses>
<license>
<name>Apache 2.0</name>
<url>https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT</url>
<distribution>repo</distribution>
</license>
</licenses>
<developers>
<developer>
<id>gatkdev</id>
<name>GATK Development Team</name>
<email>gatk-dev-public@broadinstitute.org</email>
</developer>
</developers>
<scm>
<connection>scm:git@github.com:broadinstitute/gatk.git</connection>
<developerConnection>scm:git@github.com:broadinstitute/gatk.git</developerConnection>
<url>scm:git@github.com:broadinstitute/gatk.git</url>
</scm>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java</artifactId>
<version>3.25.5</version>
</dependency>
<dependency>
<groupId>dnsjava</groupId>
<artifactId>dnsjava</artifactId>
<version>3.6.0</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>1.26.0</version>
</dependency>
<dependency>
<groupId>org.apache.ivy</groupId>
<artifactId>ivy</artifactId>
<version>2.5.2</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>1.10.0</version>
</dependency>
<dependency>
<groupId>org.apache.parquet</groupId>
<artifactId>parquet-hadoop</artifactId>
<version>1.15.1</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>1.5.13</version>
</dependency>
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
<version>1.12.0</version>
</dependency>
<dependency>
<groupId>io.airlift</groupId>
<artifactId>aircompressor</artifactId>
<version>0.27</version>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.13.14</version>
</dependency>
<dependency>
<groupId>com.nimbusds</groupId>
<artifactId>nimbus-jose-jwt</artifactId>
<version>9.41.2</version>
</dependency>
<dependency>
<groupId>org.codehaus.janino</groupId>
<artifactId>janino</artifactId>
<version>3.1.12</version>
</dependency>
<dependency>
<groupId>org.apache.zookeeper</groupId>
<artifactId>zookeeper</artifactId>
<version>3.9.2</version>
</dependency>
<dependency>
<groupId>org.jetbrains.kotlin</groupId>
<artifactId>kotlin-stdlib</artifactId>
<version>1.9.25</version>
</dependency>
<dependency>
<groupId>com.squareup.okio</groupId>
<artifactId>okio</artifactId>
<version>3.9.1</version>
</dependency>
<dependency>
<groupId>org.codehaus.jettison</groupId>
<artifactId>jettison</artifactId>
<version>1.5.4</version>
</dependency>
<dependency>
<groupId>org.xerial.snappy</groupId>
<artifactId>snappy-java</artifactId>
<version>1.1.10.4</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-bom</artifactId>
<version>2.24.1</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-bom</artifactId>
<version>4.1.118.Final</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-bom</artifactId>
<version>9.4.56.v20240826</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
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<artifactId>freemarker</artifactId>
<version>2.3.30</version>
<scope>runtime</scope>
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<dependency>
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<artifactId>barclay</artifactId>
<version>5.0.0</version>
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</dependency>
<dependency>
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<artifactId>owner</artifactId>
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<dependency>
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<artifactId>picard</artifactId>
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</dependency>
<dependency>
<groupId>org.genomicsdb</groupId>
<artifactId>genomicsdb</artifactId>
<version>1.5.5</version>
<scope>runtime</scope>
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</dependency>
<dependency>
<groupId>com.opencsv</groupId>
<artifactId>opencsv</artifactId>
<version>3.4</version>
<scope>runtime</scope>
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</dependency>
<dependency>
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<artifactId>guava</artifactId>
<version>32.1.3-jre</version>
<scope>runtime</scope>
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<dependency>
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<artifactId>htsjdk</artifactId>
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</dependency>
<dependency>
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<artifactId>google-cloud-nio</artifactId>
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</dependency>
<dependency>
<groupId>com.google.cloud</groupId>
<artifactId>google-cloud-bigquery</artifactId>
<version>2.35.0</version>
<scope>runtime</scope>
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<dependency>
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</dependency>
<dependency>
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<groupId>org.slf4j</groupId>
<artifactId>slf4j-jdk14</artifactId>
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<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
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<groupId>com.google.guava</groupId>
<artifactId>guava-jdk5</artifactId>
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<groupId>junit</groupId>
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<groupId>org.bouncycastle</groupId>
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<groupId>*</groupId>
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<groupId>*</groupId>
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<groupId>*</groupId>
<artifactId>servlet-api</artifactId>
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<exclusion>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>*</artifactId>
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</exclusions>
</dependency>
<dependency>
<groupId>org.osgi</groupId>
<artifactId>org.osgi.annotation.bundle</artifactId>
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<exclusion>
<groupId>org.slf4j</groupId>
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<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
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<groupId>com.google.guava</groupId>
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<groupId>*</groupId>
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<groupId>*</groupId>
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<groupId>*</groupId>
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<groupId>com.esotericsoftware.kryo</groupId>
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</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
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<exclusion>
<groupId>org.slf4j</groupId>
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<groupId>com.google.guava</groupId>
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<groupId>*</groupId>
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<groupId>*</groupId>
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<groupId>*</groupId>
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<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
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<groupId>org.slf4j</groupId>
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<dependency>
<groupId>org.hipparchus</groupId>
<artifactId>hipparchus-stat</artifactId>
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<exclusion>
<groupId>org.slf4j</groupId>
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<groupId>*</groupId>
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<groupId>com.esotericsoftware.kryo</groupId>
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<dependency>
<groupId>org.apache.commons</groupId>
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<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-vfs2</artifactId>
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<dependency>
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<dependency>
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<dependency>
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<dependency>
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<dependency>
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<dependency>
<groupId>org.broadinstitute</groupId>
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<dependency>
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<dependency>
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<dependency>
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<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
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<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava-jdk5</artifactId>
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<exclusion>
<groupId>junit</groupId>
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<exclusion>
<groupId>org.bouncycastle</groupId>
<artifactId>bcprov-jdk15on</artifactId>
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<exclusion>
<groupId>*</groupId>
<artifactId>jul-to-slf4j</artifactId>
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<exclusion>
<groupId>*</groupId>
<artifactId>javax.servlet</artifactId>
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<exclusion>
<groupId>*</groupId>
<artifactId>servlet-api</artifactId>
</exclusion>
<exclusion>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>*</artifactId>
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</exclusions>
</dependency>
<dependency>
<groupId>org.disq-bio</groupId>
<artifactId>disq</artifactId>
<version>0.3.8</version>
<scope>runtime</scope>
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<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-jdk14</artifactId>
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<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
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<exclusion>
<groupId>com.google.guava</groupId>
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</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-client</artifactId>
<version>3.3.6</version>
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<exclusion>
<groupId>org.slf4j</groupId>
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</dependency>
<dependency>
<groupId>com.github.jsr203hadoop</groupId>
<artifactId>jsr203hadoop</artifactId>
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<exclusion>
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</dependency>
<dependency>
<groupId>org.apache.orc</groupId>
<artifactId>orc</artifactId>
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<scope>runtime</scope>
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<exclusion>
<groupId>org.slf4j</groupId>
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</dependency>
<dependency>
<groupId>de.javakaffee</groupId>
<artifactId>kryo-serializers</artifactId>
<version>0.45</version>
<scope>runtime</scope>
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<exclusion>
<groupId>org.slf4j</groupId>
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</dependency>
<dependency>
<groupId>com.esotericsoftware</groupId>
<artifactId>kryo</artifactId>
<version>[4,5)</version>
<scope>runtime</scope>
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<exclusion>
<groupId>org.slf4j</groupId>
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</dependency>
<dependency>
<groupId>org.objenesis</groupId>
<artifactId>objenesis</artifactId>
<version>1.2</version>
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<exclusion>
<groupId>org.slf4j</groupId>
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</dependency>
<dependency>
<groupId>com.github.fommil.netlib</groupId>
<artifactId>netlib-native_ref-osx-x86_64</artifactId>
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<classifier>natives</classifier>
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<artifactId>servlet-api</artifactId>
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<dependency>
<groupId>com.github.fommil.netlib</groupId>
<artifactId>netlib-native_ref-linux-x86_64</artifactId>
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<classifier>natives</classifier>
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<groupId>org.slf4j</groupId>
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<artifactId>javax.servlet</artifactId>
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<groupId>*</groupId>
<artifactId>servlet-api</artifactId>
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<exclusion>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>*</artifactId>
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</exclusions>
</dependency>
<dependency>
<groupId>com.github.fommil.netlib</groupId>
<artifactId>netlib-native_system-linux-x86_64</artifactId>
<version>1.1</version>
<classifier>natives</classifier>
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<exclusion>
<groupId>*</groupId>
<artifactId>javax.servlet</artifactId>
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<exclusion>
<groupId>*</groupId>
<artifactId>servlet-api</artifactId>
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<exclusion>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>*</artifactId>
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</dependency>
<dependency>
<groupId>com.github.fommil.netlib</groupId>
<artifactId>netlib-native_system-osx-x86_64</artifactId>
<version>1.1</version>
<classifier>natives</classifier>
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<groupId>*</groupId>
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<groupId>*</groupId>
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<groupId>*</groupId>
<artifactId>servlet-api</artifactId>
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</dependency>
<dependency>
<groupId>com.intel.gkl</groupId>
<artifactId>gkl</artifactId>
<version>0.8.11</version>
<scope>runtime</scope>
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<exclusion>
<groupId>org.slf4j</groupId>
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<dependency>
<groupId>org.broadinstitute</groupId>
<artifactId>gatk-bwamem-jni</artifactId>
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<scope>runtime</scope>
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<groupId>*</groupId>
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</dependency>
<dependency>
<groupId>org.broadinstitute</groupId>
<artifactId>http-nio</artifactId>
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<scope>runtime</scope>
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</dependency>
<dependency>
<groupId>org.xerial</groupId>
<artifactId>sqlite-jdbc</artifactId>
<version>3.44.1.0</version>
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</dependency>
<dependency>
<groupId>net.grey-panther</groupId>
<artifactId>natural-comparator</artifactId>
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</dependency>
<dependency>
<groupId>com.fasterxml.jackson.module</groupId>
<artifactId>jackson-module-scala_2.13</artifactId>
<version>2.9.8</version>
<scope>runtime</scope>
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<exclusion>
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<exclusion>
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<artifactId>servlet-api</artifactId>
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<exclusion>
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<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
</project>
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