diff --git a/README.md b/README.md
index d4236dd8..6f814507 100644
--- a/README.md
+++ b/README.md
@@ -19,10 +19,7 @@ Avocado is currently in its infancy, but we hope to have something interesting t
 
 ## Building avocado
 
-avocado uses [sbt](http://www.scala-sbt.org/) to build. To build avocado, cd into the repository and run "sbt compile".
+avocado uses [Maven](http://maven.apache.org/) to build. To build avocado, cd into the repository and run "mvn package".
 
 Known issues with building:
-* There is a current issue where the first time that the project is built, it fails on the first build before succeeding on the second build. This is because of an issue with a local dependency, that should hopefully be fixed soon.
-* And... that local dependency is Adam. To install Adam locally, check out Adam and do "mvn package install" (for build instructions, see [the Adam readme](https://github.com/bigdatagenomics/adam)). We are picky though: currently, avocado depends on an Adam pull request that hasn't merged in yet. This pull request is available as the "avocado-patch" branch at [fnothaft/adam](https://github.com/fnothaft/adam).
-
-Standalone JARs are built using [sbt assembly](https://github.com/sbt/sbt-assembly). Once you have compiled, you can build the JAR by running "sbt assembly". Currently, the initial JAR takes about 10 minutes to build, but YMMV.
\ No newline at end of file
+* This project requires Adam as a local dependency. To install Adam locally, check out Adam and do "mvn package install" (for build instructions, see [the Adam readme](https://github.com/bigdatagenomics/adam)). We build off of the Adam trunk.
diff --git a/build.sbt b/build.sbt
deleted file mode 100644
index fdc149b6..00000000
--- a/build.sbt
+++ /dev/null
@@ -1,53 +0,0 @@
-import AssemblyKeys._
-
-assemblySettings
-
-name := "Avocado"
-
-version := "0.0.1"
-
-organization := "edu.berkeley.cs.amplab"
-
-scalaVersion := "2.9.3"
-
-classpathTypes ++= Set ("orbit")
-
-net.virtualvoid.sbt.graph.Plugin.graphSettings
-
-libraryDependencies ++= Seq(
-  "org.apache.spark" %% "spark-core" % "0.8.0-incubating",
-  "org.scalatest" %% "scalatest" % "1.9.1" % "test",
-  "edu.berkeley.cs.amplab.adam" % "adam-format" % "0.5.0-SNAPSHOT",
-  "edu.berkeley.cs.amplab.adam" % "adam-commands" % "0.5.0-SNAPSHOT",
-  "args4j" % "args4j" % "2.0.23",
-  "commons-lang" % "commons-lang" % "2.6",
-  "variant" % "variant" % "1.93",
-  "tribble" % "tribble" % "1.93"
-)
-
-libraryDependencies ++= Seq(
-  "org.eclipse.jetty.orbit" % "javax.servlet" % "2.5.0.v201103041518" artifacts (Artifact("javax.servlet", "jar", "jar")
-  )
-)
-
-resolvers ++= Seq(
-  "Typesafe" at "http://repo.typesafe.com/typesafe/releases",
-  "Scala Tools Snapshots" at "http://scala-tools.org/repo-snapshots/",
-  "Spray" at "http://repo.spray.cc",
-  "Local" at "file:///Users/fnothaft/.m2/repository",
-  "massie-maven" at "http://www.cs.berkeley.edu/~massie/maven/",
-  "apache" at "https://repository.apache.org/content/repositories/releases",
-  "hadoop-bam" at "http://hadoop-bam.sourceforge.net/maven/"
-)
-
-mergeStrategy in assembly := {
- case m if m.toLowerCase.endsWith("manifest.mf") => MergeStrategy.discard
- case m if m.toLowerCase.matches("meta-inf.*\\.sf$") => MergeStrategy.discard
- case "META-INF/services/org.apache.hadoop.fs.FileSystem" =>
-MergeStrategy.concat
- case "reference.conf" => MergeStrategy.concat
- case "log4j.properties" => MergeStrategy.concat
- case _ => MergeStrategy.first
-}
-
-assemblyCacheOutput in assembly := false
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 00000000..76daa118
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,129 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <groupId>edu.berkeley.cs.amplab.avocado</groupId>
+    <artifactId>avocado</artifactId>
+    <version>0.0.1</version>
+    <packaging>jar</packaging>
+    <name>avocado: A Variant Caller, Distributed</name>
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>2.1</version>
+                <configuration>
+                    <transformers>
+                        <transformer
+                                implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                            <mainClass>edu.berkeley.cs.amplab.avocado.Avocado</mainClass>
+                        </transformer>
+                        <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+                            <resource>reference.conf</resource>
+                        </transformer>
+                    </transformers>
+                    <finalName>avocado-${project.version}</finalName>
+                    <filters>
+                        <filter>
+                            <artifact>*:*</artifact>
+                            <excludes>
+                                <exclude>META-INF/*.SF</exclude>
+                                <exclude>META-INF/*.DSA</exclude>
+                                <exclude>META-INF/*.RSA</exclude>
+                                <exclude>META-INF/LICENSE</exclude>
+                                <exclude>META-INF/license</exclude>
+                            </excludes>
+                        </filter>
+                    </filters>
+                    <artifactSet>
+                        <excludes>
+                            <exclude>org.eclipse.jdt:*</exclude>
+                            <exclude>org.scalatest:*</exclude>
+                            <exclude>org.apache.maven:lib:tests</exclude>
+                        </excludes>
+                    </artifactSet>
+                </configuration>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>net.alchim31.maven</groupId>
+                <artifactId>scala-maven-plugin</artifactId>
+                <version>3.1.5</version>
+                <executions>
+                    <execution>
+                        <id>scala-compile-first</id>
+                        <phase>process-resources</phase>
+                        <goals>
+                            <goal>compile</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>scala-test-compile-first</id>
+                        <phase>process-test-resources</phase>
+                        <goals>
+                            <goal>testCompile</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>attach-scaladocs</id>
+                        <phase>verify</phase>
+                        <goals>
+                            <goal>doc-jar</goal>
+                        </goals>
+                    </execution>
+                </executions>
+                <configuration>
+                    <scalaVersion>${scala.version}</scalaVersion>
+                    <recompileMode>incremental</recompileMode>
+                    <useZincServer>true</useZincServer>
+                    <args>
+                        <arg>-unchecked</arg>
+                        <arg>-optimise</arg>
+                        <arg>-deprecation</arg>
+                    </args>
+                    <jvmArgs>
+                        <jvmArg>-Xms64m</jvmArg>
+                        <jvmArg>-Xms1024m</jvmArg>
+                        <jvmArg>-Xmx1024m</jvmArg>
+                    </jvmArgs>
+                    <javacArgs>
+                        <javacArg>-source</javacArg>
+                        <javacArg>${java.version}</javacArg>
+                        <javacArg>-target</javacArg>
+                        <javacArg>${java.version}</javacArg>
+                    </javacArgs>
+                </configuration>
+            </plugin>
+            <!-- disable surefire -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>2.7</version>
+                <configuration>
+                    <skipTests>true</skipTests>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <dependencies>
+        <dependency>
+            <groupId>edu.berkeley.cs.amplab.adam</groupId>
+            <artifactId>adam-format</artifactId>
+            <version>0.5.0-SNAPSHOT</version>
+        </dependency>
+        <dependency>
+            <groupId>edu.berkeley.cs.amplab.adam</groupId>
+            <artifactId>adam-commands</artifactId>
+            <version>0.5.0-SNAPSHOT</version>
+        </dependency>
+    </dependencies>
+</project>
diff --git a/project/build.properties b/project/build.properties
deleted file mode 100644
index 45ec8a69..00000000
--- a/project/build.properties
+++ /dev/null
@@ -1 +0,0 @@
-sbt.version = 0.12.4
\ No newline at end of file
diff --git a/project/plugins.sbt b/project/plugins.sbt
deleted file mode 100644
index 981d163f..00000000
--- a/project/plugins.sbt
+++ /dev/null
@@ -1,4 +0,0 @@
-addSbtPlugin("net.virtual-void" % "sbt-dependency-graph" % "0.7.4")
-
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.9.2")
-