diff --git a/public/java/src/org/broadinstitute/sting/datasources/pipeline/Pipeline.java b/public/java/src/org/broadinstitute/sting/pipeline/Pipeline.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/datasources/pipeline/Pipeline.java
rename to public/java/src/org/broadinstitute/sting/pipeline/Pipeline.java
index f8f8b2d29..e0e75c353 100644
--- a/public/java/src/org/broadinstitute/sting/datasources/pipeline/Pipeline.java
+++ b/public/java/src/org/broadinstitute/sting/pipeline/Pipeline.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.datasources.pipeline;
+package org.broadinstitute.sting.pipeline;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java b/public/java/src/org/broadinstitute/sting/pipeline/PipelineProject.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java
rename to public/java/src/org/broadinstitute/sting/pipeline/PipelineProject.java
index 7967ba5df..8d33047bf 100644
--- a/public/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java
+++ b/public/java/src/org/broadinstitute/sting/pipeline/PipelineProject.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.datasources.pipeline;
+package org.broadinstitute.sting.pipeline;
 
 import java.io.File;
 import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineSample.java b/public/java/src/org/broadinstitute/sting/pipeline/PipelineSample.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineSample.java
rename to public/java/src/org/broadinstitute/sting/pipeline/PipelineSample.java
index 701841302..7cd25fed5 100644
--- a/public/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineSample.java
+++ b/public/java/src/org/broadinstitute/sting/pipeline/PipelineSample.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.datasources.pipeline;
+package org.broadinstitute.sting.pipeline;
 
 import java.io.File;
 import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/utils/broad/PicardAggregationUtils.java b/public/java/src/org/broadinstitute/sting/utils/broad/PicardAggregationUtils.java
deleted file mode 100755
index 8f3ffd741..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/broad/PicardAggregationUtils.java
+++ /dev/null
@@ -1,149 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.broad;
-
-import org.apache.commons.io.filefilter.RegexFileFilter;
-
-import java.io.File;
-import java.io.FileFilter;
-import java.io.FileNotFoundException;
-import java.util.Arrays;
-
-public class PicardAggregationUtils {
-    public static final String PICARD_AGGREGATION_DIR = "/seq/picard_aggregation/";
-
-    /**
-     * Returns the path to the sample BAM.
-     * @param project Project
-     * @param sample Sample
-     * @param version Version
-     * @return The path to the sample BAM.
-     */
-    public static String getSampleBam(String project, String sample, int version) {
-        return getSampleDir(project, sample, version) + sample + ".bam";
-    }
-
-    /**
-     * Returns the path to the latest BAM.
-     * @param project Project
-     * @param sample Sample
-     * @return The path to the latest BAM.
-     * @throws FileNotFoundException If a finished directory cannot be found for a sample.
-     */
-    public static String getSampleBam(String project, String sample) throws FileNotFoundException {
-        return getSampleDir(project, sample) + sample + ".bam";
-    }
-
-    /**
-     * Returns the sample directory.
-     * @param project Project
-     * @param sample Sample
-     * @param version Version
-     * @return the sample directory.
-     */
-    public static String getSampleDir(String project, String sample, int version) {
-        return PICARD_AGGREGATION_DIR + String.format("%s/%s/v%d/", project, sample, version);
-    }
-
-    /**
-     * Returns the latest finished directory for this project sample.
-     * @param project Project
-     * @param sample Sample
-     * @return The path to the latest finished directory.
-     * @throws FileNotFoundException If a finished directory cannot be found for a sample.
-     */
-    public static String getSampleDir(String project, String sample) throws FileNotFoundException {
-        int latestVersion = getLatestVersion(project, sample);
-        if (latestVersion == 0)
-            throw new FileNotFoundException("Unable to find a finished directory for project sample " + project + "/" + sample);
-        return getSampleDir(project, sample, latestVersion);
-    }
-
-    /**
-     * Returns the latest finished version directory.
-     * Because isilon metadata operations are relatively slow this method
-     * tries not to look for every possible versioned directory.
-     * @param project Project
-     * @param sample Sample
-     * @return The highest finished version directory or 0 if a finished directory was not found.
-     */
-    public static int getLatestVersion(String project, String sample) {
-        return getLatestVersion(project, sample, 0);
-    }
-
-    /**
-     * Returns the latest finished version directory after startVersion.
-     * Because isilon metadata operations are relatively slow this method
-     * tries not to look for every possible versioned directory.
-     * @param project Project
-     * @param sample Sample
-     * @param startVersion minimum version to return
-     * @return The highest finished version directory after startVersion
-     */
-    public static int getLatestVersion(String project, String sample, int startVersion) {
-        int version = Math.max(0, startVersion);
-        boolean nextExists = true;
-        while (nextExists) {
-            nextExists = false;
-            for (int next = 3; next > 0; next--)
-                if (isFinished(project, sample, version + next)) {
-                    version += next;
-                    nextExists = true;
-                    break;
-                }
-        }
-        // Special case when the version is 0
-        // Because isilon storage takes a while to do meta data operations only look through every file if we have to.
-        if (version == 0) {
-            File sampleDir = new File(PICARD_AGGREGATION_DIR + project + "/" + sample);
-            if (sampleDir.exists()) {
-                FileFilter filter = new RegexFileFilter("v\\d+");
-                File[] files = sampleDir.listFiles(filter);
-                int[] versions = new int[files.length];
-                for (int i = 0; i < files.length; i++)
-                    versions[i] = Integer.parseInt(files[i].getName().substring(1));
-                Arrays.sort(versions);
-                for (int i = versions.length - 1; i >= 0; i--) {
-                    if (isFinished(project, sample, versions[i])) {
-                        version = versions[i];
-                        break;
-                    }
-                }
-            }
-        }
-        return version == 0 ? startVersion : version;
-    }
-
-    /**
-     * Returns true if the project sample directory contains a finished.txt
-     * @param project Project
-     * @param sample Sample
-     * @param version Version
-     * @return true if the project sample directory contains a finished.txt
-     */
-    public static boolean isFinished(String project, String sample, int version) {
-        return new File(getSampleDir(project, sample, version), "finished.txt").exists();
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/broad/PicardAnalysisFiles.java b/public/java/src/org/broadinstitute/sting/utils/broad/PicardAnalysisFiles.java
deleted file mode 100755
index 02381916e..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/broad/PicardAnalysisFiles.java
+++ /dev/null
@@ -1,108 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.broad;
-
-import org.apache.commons.lang.ArrayUtils;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.text.XReadLines;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-public class PicardAnalysisFiles {
-    private static final String REFERENCE_SEQUENCE_HEADER = "REFERENCE_SEQUENCE";
-    private static final String TARGET_INTERVALS_HEADER = "TARGET_INTERVALS";
-    private static final String BAIT_INTERVALS_HEADER = "BAIT_INTERVALS";
-    private static final String[] ANALYSIS_HEADERS = {REFERENCE_SEQUENCE_HEADER, TARGET_INTERVALS_HEADER, BAIT_INTERVALS_HEADER};
-    private static final String ANALYSIS_FILES = "analysis_files.txt";
-
-    private String path;
-    private Map<String,Set<String>> headerValues = new HashMap<String,Set<String>>();
-
-    public PicardAnalysisFiles(String project, String sample) throws FileNotFoundException {
-        this(PicardAggregationUtils.getSampleDir(project, sample) + ANALYSIS_FILES);
-    }
-
-    public PicardAnalysisFiles(String project, String sample, int version) throws FileNotFoundException {
-        this(PicardAggregationUtils.getSampleDir(project, sample, version) + ANALYSIS_FILES);
-    }
-
-    public PicardAnalysisFiles(String path) throws FileNotFoundException {
-        this.path = path;
-        HashMap<String,Integer> headerIndexes = null;
-        for (String line: new XReadLines(new File(path))) {
-            if (line.startsWith("#"))
-                continue;
-            String[] values = line.split("\t");
-            if (headerIndexes == null) {
-                headerIndexes = new HashMap<String,Integer>();
-                for (String header: ANALYSIS_HEADERS) {
-                    headerIndexes.put(header, ArrayUtils.indexOf(values, header));
-                    headerValues.put(header, new HashSet<String>());
-                }
-            } else {
-                for (String header: ANALYSIS_HEADERS) {
-                    int index = headerIndexes.get(header);
-                    if (values.length <= index)
-                        throw new StingException(String.format("Unable to parse line in %s: %n%s", path, line));
-                    String value = values[index];
-                    headerValues.get(header).add(value);
-                }
-            }
-        }
-    }
-
-    public String getPath() {
-        return path;
-    }
-
-    public String getReferenceSequence() {
-        return getSingle(REFERENCE_SEQUENCE_HEADER);
-    }
-
-    public String getTargetIntervals() {
-        return getSingle(TARGET_INTERVALS_HEADER);
-    }
-
-    public String getBaitIntervals() {
-        return getSingle(BAIT_INTERVALS_HEADER);
-    }
-
-    private String getSingle(String header) {
-        Set<String> values = headerValues.get(header);
-        if (values.size() > 1) {
-            throw new UnsupportedOperationException(path + " contains more than one value for " + header + ": " + values);
-        } else if (values.size() == 0) {
-            return null;
-        } else {
-            String value = values.iterator().next();
-            return "null".equals(value) ? null : value;
-        }
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/broad/PicardPipeline.java b/public/java/src/org/broadinstitute/sting/utils/broad/PicardPipeline.java
deleted file mode 100755
index 96bbb2455..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/broad/PicardPipeline.java
+++ /dev/null
@@ -1,123 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.broad;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.lang.NullArgumentException;
-import org.broadinstitute.sting.datasources.pipeline.Pipeline;
-import org.broadinstitute.sting.datasources.pipeline.PipelineProject;
-import org.broadinstitute.sting.datasources.pipeline.PipelineSample;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.yaml.YamlUtils;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-
-/**
- * Automatically gets the latest version using PicardAggregationUtils.
- */
-public class PicardPipeline {
-
-    protected static final String PROJECT_TAG = "SQUIDProject";
-    protected static final String SAMPLE_TAG = "CollaboratorID";
-    protected static final String PICARD_BAM_TYPE = "cleaned";
-
-    private PicardPipeline() {}
-
-    /**
-     * Creates a new PicardPipeline
-     * @param path Path to a tsv with project [tab] sample on each line or a pipeline yaml.
-     * @return a new Picard
-     * @throws FileNotFoundException when unable to find the file or any supporting files.
-     */
-    public static Pipeline parse(File path) throws FileNotFoundException {
-        if (path == null)
-            throw new NullArgumentException("path");
-
-        Pipeline pipeline;
-        if (path.getName().endsWith(".tsv")) {
-            pipeline = new Pipeline();
-            pipeline.getProject().setName(FilenameUtils.getBaseName(path.getPath()));
-            for (String line: new XReadLines(path)) {
-                String[] projectSample = line.split("\t");
-                addSample(pipeline, projectSample[0], projectSample[1]);
-            }
-        } else if (path.getName().endsWith(".yaml")) {
-            pipeline = YamlUtils.load(Pipeline.class, path);
-        } else {
-            throw new UserException.BadInput("Path does not end with .tsv or .yaml: " + path.getPath());
-        }
-
-        update(pipeline);
-        return pipeline;
-    }
-
-    private static void update(Pipeline pipeline) throws FileNotFoundException {
-        for (PipelineSample sample: pipeline.getSamples())
-            updateSample(pipeline.getProject(), sample);
-    }
-
-    private static void addSample(Pipeline pipeline, String project, String sample) {
-        PipelineSample pipelineSample = new PipelineSample();
-        pipelineSample.getTags().put(PROJECT_TAG, project);
-        pipelineSample.getTags().put(SAMPLE_TAG, sample);
-        pipeline.getSamples().add(pipelineSample);
-    }
-
-    private static void updateSample(PipelineProject pipelineProject, PipelineSample pipelineSample) throws FileNotFoundException {
-        if (!pipelineSample.getTags().containsKey(PROJECT_TAG) && !pipelineSample.getTags().containsKey(SAMPLE_TAG))
-            return;
-        String project = pipelineSample.getTags().get(PROJECT_TAG);
-        String sample = pipelineSample.getTags().get(SAMPLE_TAG);
-        int version = PicardAggregationUtils.getLatestVersion(project, sample);
-        if (version <= 0)
-            throw new UserException.BadInput("Project sample not found: " + project + "/" + sample);
-        String bam = PicardAggregationUtils.getSampleBam(project, sample, version);
-        if (pipelineSample.getId() == null)
-            pipelineSample.setId(project + "_" + sample);
-        pipelineSample.getBamFiles().put(PICARD_BAM_TYPE, new File(bam));
-
-        PicardAnalysisFiles analysis = new PicardAnalysisFiles(project, sample, version);
-        if (pipelineProject.getReferenceFile() == null) {
-            String referenceSequence = analysis.getReferenceSequence();
-            ReferenceData referenceData = ReferenceData.getByReference(referenceSequence);
-            pipelineProject.setReferenceFile(new File(referenceData.getReference()));
-            pipelineProject.setRefseqTable(new File(referenceData.getRefseq()));
-            if (analysis.getTargetIntervals() != null)
-                pipelineProject.setIntervalList(new File(analysis.getTargetIntervals()));
-            pipelineProject.setEvalDbsnp(new File(referenceData.getDbsnp(129)));
-            if (referenceData.getDbsnpVersions().contains(132)) {
-                pipelineProject.setGenotypeDbsnp(new File(referenceData.getDbsnp(132)));
-            } else {
-                pipelineProject.setGenotypeDbsnp(new File(referenceData.getDbsnp(129)));
-            }
-        } else {
-            String referenceSequence = analysis.getReferenceSequence();
-            if (!pipelineProject.getReferenceFile().getPath().equals(referenceSequence))
-                throw new UserException.BadInput("Samples sequenced with different references");
-        }
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/broad/ReferenceData.java b/public/java/src/org/broadinstitute/sting/utils/broad/ReferenceData.java
deleted file mode 100755
index 36a59ec70..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/broad/ReferenceData.java
+++ /dev/null
@@ -1,135 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.broad;
-
-import java.util.Collections;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-/**
- * Tracks data related to reference files at the Broad.
- */
-public enum ReferenceData {
-    /**
-     * HG18 reference data
-     */
-    HG18("hg18"),
-
-    /**
-     * HG19 reference data
-     */
-    HG19("hg19");
-
-    private static final String REFSEQ_DIR = "/humgen/gsa-hpprojects/GATK/data/Annotations/refseq/";
-    private static final String DBSNP_DIR = "/humgen/gsa-hpprojects/GATK/data/";
-
-    private final String name;
-    private final String reference;
-    private final String refseq;
-    private final Map<Integer,String> dbsnps;
-
-    ReferenceData(String name) {
-        this.name = name;
-        Map<Integer,String> dbsnps = new TreeMap<Integer,String>();
-        if ("hg18".equals(name)) {
-            this.reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
-            this.refseq = REFSEQ_DIR + "refGene-big-table-hg18.txt";
-            dbsnps.put(129, DBSNP_DIR + "dbsnp_129_hg18.rod");
-        } else if ("hg19".equals(name)) {
-            this.reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
-            this.refseq = REFSEQ_DIR + "refGene-big-table-hg19.txt";
-            dbsnps.put(129, DBSNP_DIR + "dbsnp_129_b37.vcf");
-            dbsnps.put(132, DBSNP_DIR + "dbsnp_132_b37.vcf");
-        } else
-            throw new UnsupportedOperationException("Unknown reference: " + name);
-        this.dbsnps = Collections.unmodifiableMap(dbsnps);
-    }
-
-    /**
-     * Returns the name of the reference.
-     * @return the name of the reference.
-     */
-    public String getName() {
-        return name;
-    }
-
-    /**
-     * Returns the path to the fasta.
-     * @return the path to the fasta.
-     */
-    public String getReference() {
-        return reference;
-    }
-
-    /**
-     * Returns the path to the refseq table.
-     * @return the path to the refseq table.
-     */
-    public String getRefseq() {
-        return refseq;
-    }
-
-    /**
-     * Returns the dbsnp versions available.
-     * @return the dbsnp versions available.
-     */
-    public Set<Integer> getDbsnpVersions() {
-        return dbsnps.keySet();
-    }
-
-    /**
-     * Returns the dbsnp path for the version.
-     * @param version version from getDbsnpVersions()
-     * @return the dbsnp path for the version.
-     */
-    public String getDbsnp(int version) {
-        return dbsnps.get(version);
-    }
-
-    /**
-     * Returns the dbsnp type for the version, "VCF" or "DBSNP".
-     * @param version version from getDbsnpVersions()
-     * @return the dbsnp type for the version, "VCF" or "DBSNP".
-     */
-    public String getDbsnpType(int version) {
-        String dbsnp = getDbsnp(version);
-        if (dbsnp == null)
-            return null;
-        return dbsnp.toLowerCase().endsWith(".vcf") ? "VCF" : "DBSNP";
-    }
-
-    /**
-     * Returns the reference data based on the path or null.
-     * @param reference path to the reference
-     * @return the reference data based on the path or null.
-     */
-    public static ReferenceData getByReference(String reference) {
-        for (ReferenceData data: ReferenceData.values())
-            if (data.reference.equals(reference))
-                return data;
-        return null;
-    }
-}
diff --git a/public/java/test/org/broadinstitute/sting/datasources/pipeline/PipelineUnitTest.java b/public/java/test/org/broadinstitute/sting/pipeline/PipelineUnitTest.java
similarity index 96%
rename from public/java/test/org/broadinstitute/sting/datasources/pipeline/PipelineUnitTest.java
rename to public/java/test/org/broadinstitute/sting/pipeline/PipelineUnitTest.java
index 8e18fac6f..891356670 100644
--- a/public/java/test/org/broadinstitute/sting/datasources/pipeline/PipelineUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/pipeline/PipelineUnitTest.java
@@ -22,8 +22,10 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.datasources.pipeline;
+package org.broadinstitute.sting.pipeline;
 
+import org.broadinstitute.sting.pipeline.Pipeline;
+import org.broadinstitute.sting.pipeline.PipelineSample;
 import org.testng.Assert;
 import org.broadinstitute.sting.utils.yaml.YamlUtils;
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/broad/PicardAggregationUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/broad/PicardAggregationUtilsUnitTest.java
deleted file mode 100755
index 77a8a1ac8..000000000
--- a/public/java/test/org/broadinstitute/sting/utils/broad/PicardAggregationUtilsUnitTest.java
+++ /dev/null
@@ -1,61 +0,0 @@
-package org.broadinstitute.sting.utils.broad;
-
-import org.testng.Assert;
-import org.testng.annotations.Test;
-
-import java.io.FileNotFoundException;
-
-public class PicardAggregationUtilsUnitTest {
-    public static final String PROJECT = "C474";
-    public static final String SAMPLE = "NA19651";
-    public static final String MISSING_PROJECT = "C0";
-    public static final String MISSING_SAMPLE = "0";
-    private int latestVersion = -1;
-
-    @Test
-    public void testGetLatestVersion() {
-        latestVersion = PicardAggregationUtils.getLatestVersion(PROJECT, SAMPLE);
-        System.out.println(String.format("Latest version for %s %s is %d", PROJECT, SAMPLE, latestVersion));
-        Assert.assertTrue(latestVersion > 0);
-        Assert.assertEquals(PicardAggregationUtils.getLatestVersion(PROJECT, SAMPLE, latestVersion), latestVersion);
-    }
-
-    @Test(dependsOnMethods = "testGetLatestVersion")
-    public void testGetSampleBam() throws Exception {
-        String test = PicardAggregationUtils.getSampleBam(PROJECT, SAMPLE);
-        String latest = PicardAggregationUtils.getSampleBam(PROJECT, SAMPLE, latestVersion);
-        Assert.assertEquals(test, latest);
-    }
-
-    @Test(dependsOnMethods = "testGetLatestVersion")
-    public void testGetSampleDir() throws Exception {
-        String test = PicardAggregationUtils.getSampleDir(PROJECT, SAMPLE);
-        String latest = PicardAggregationUtils.getSampleDir(PROJECT, SAMPLE, latestVersion);
-        Assert.assertEquals(test, latest);
-    }
-
-    @Test(dependsOnMethods = "testGetLatestVersion")
-    public void testIsFinished() {
-        Assert.assertTrue(PicardAggregationUtils.isFinished(PROJECT, SAMPLE, latestVersion));
-        Assert.assertFalse(PicardAggregationUtils.isFinished(PROJECT, SAMPLE, latestVersion + 1));
-    }
-
-    @Test(expectedExceptions = FileNotFoundException.class)
-    public void testMissingSampleBam() throws Exception {
-        PicardAggregationUtils.getSampleBam(MISSING_PROJECT, MISSING_SAMPLE);
-    }
-
-    @Test(expectedExceptions = FileNotFoundException.class)
-    public void testMissingSampleDir() throws Exception {
-        PicardAggregationUtils.getSampleDir(MISSING_PROJECT, MISSING_SAMPLE);
-    }
-
-    @Test
-    public void testLatestVersionMissing() {
-        Assert.assertEquals(PicardAggregationUtils.getLatestVersion(MISSING_PROJECT, MISSING_SAMPLE), 0);
-        Assert.assertEquals(PicardAggregationUtils.getLatestVersion(MISSING_PROJECT, MISSING_SAMPLE, -1), -1);
-        Assert.assertEquals(PicardAggregationUtils.getLatestVersion(MISSING_PROJECT, MISSING_SAMPLE, 0), 0);
-        Assert.assertEquals(PicardAggregationUtils.getLatestVersion(MISSING_PROJECT, MISSING_SAMPLE, 1), 1);
-        Assert.assertEquals(PicardAggregationUtils.getLatestVersion(MISSING_PROJECT, MISSING_SAMPLE, 2), 2);
-    }
-}
diff --git a/public/java/test/org/broadinstitute/sting/utils/broad/PicardAnalysisFilesUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/broad/PicardAnalysisFilesUnitTest.java
deleted file mode 100755
index de58bf983..000000000
--- a/public/java/test/org/broadinstitute/sting/utils/broad/PicardAnalysisFilesUnitTest.java
+++ /dev/null
@@ -1,56 +0,0 @@
-package org.broadinstitute.sting.utils.broad;
-
-import org.broadinstitute.sting.BaseTest;
-import org.testng.Assert;
-import org.testng.annotations.Test;
-
-import java.io.FileNotFoundException;
-
-import static org.broadinstitute.sting.utils.broad.PicardAggregationUtilsUnitTest.*;
-
-public class PicardAnalysisFilesUnitTest extends BaseTest {
-    @Test
-    public void testParseLatest() throws Exception {
-        PicardAnalysisFiles files = new PicardAnalysisFiles(PROJECT, SAMPLE);
-        Assert.assertNotNull(files.getPath());
-        files = new PicardAnalysisFiles(PROJECT, SAMPLE, PicardAggregationUtils.getLatestVersion(PROJECT, SAMPLE));
-        Assert.assertNotNull(files.getPath());
-    }
-
-    @Test
-    public void testParseValid() throws Exception {
-        PicardAnalysisFiles file = new PicardAnalysisFiles(BaseTest.validationDataLocation + "picard_analysis_file.txt");
-        Assert.assertEquals(file.getReferenceSequence(), "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta");
-        Assert.assertEquals(file.getTargetIntervals(), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list");
-        Assert.assertEquals(file.getBaitIntervals(), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list");
-    }
-
-    @Test
-    public void testParseValidWithComments() throws Exception {
-        PicardAnalysisFiles file = new PicardAnalysisFiles(BaseTest.validationDataLocation + "picard_analysis_file_with_comments.txt");
-        Assert.assertEquals(file.getReferenceSequence(), "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta");
-        Assert.assertEquals(file.getTargetIntervals(), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list");
-        Assert.assertEquals(file.getBaitIntervals(), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list");
-    }
-
-    @Test(expectedExceptions = FileNotFoundException.class)
-    public void testParseBadPath() throws Exception {
-        new PicardAnalysisFiles(BaseTest.validationDataLocation + "non_existent_picard_analysis_file.txt");
-    }
-
-    @Test(expectedExceptions = FileNotFoundException.class)
-    public void testParseMissingLatest() throws Exception {
-        new PicardAnalysisFiles(MISSING_PROJECT, MISSING_SAMPLE);
-    }
-
-    @Test(expectedExceptions = FileNotFoundException.class)
-    public void testParseMissingVersion() throws Exception {
-        new PicardAnalysisFiles(PROJECT, SAMPLE, PicardAggregationUtils.getLatestVersion(PROJECT, SAMPLE) + 2);
-    }
-
-    @Test(expectedExceptions = UnsupportedOperationException.class)
-    public void testParseMultipleReferences() throws Exception {
-        PicardAnalysisFiles file = new PicardAnalysisFiles(BaseTest.validationDataLocation + "picard_analysis_file_with_different_references.txt");
-        file.getReferenceSequence();
-    }
-}
diff --git a/public/java/test/org/broadinstitute/sting/utils/broad/PicardPipelineUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/broad/PicardPipelineUnitTest.java
deleted file mode 100755
index 121ca4619..000000000
--- a/public/java/test/org/broadinstitute/sting/utils/broad/PicardPipelineUnitTest.java
+++ /dev/null
@@ -1,71 +0,0 @@
-package org.broadinstitute.sting.utils.broad;
-
-import org.testng.Assert;
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.FilenameUtils;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.datasources.pipeline.Pipeline;
-import org.broadinstitute.sting.datasources.pipeline.PipelineSample;
-import org.broadinstitute.sting.utils.yaml.YamlUtils;
-import org.testng.annotations.Test;
-import static org.broadinstitute.sting.utils.broad.PicardAggregationUtilsUnitTest.*;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Collections;
-
-public class PicardPipelineUnitTest {
-    @Test
-    public void testParseTsv() throws IOException {
-        File tsv = writeTsv(PROJECT, SAMPLE);
-        Pipeline pipeline = PicardPipeline.parse(tsv);
-        validatePipeline(pipeline, FilenameUtils.getBaseName(tsv.getPath()));
-    }
-
-    @Test
-    public void testParseTsvWithPicardComments() throws Exception {
-        File tsv = writeTsv("C460", "HG01359");
-        PicardPipeline.parse(tsv);
-    }
-
-    @Test
-    public void testParseYaml() throws IOException {
-        File yaml = writeYaml("project_name", PROJECT, SAMPLE);
-        Pipeline pipeline = PicardPipeline.parse(yaml);
-        validatePipeline(pipeline, "project_name");
-    }
-
-    private void validatePipeline(Pipeline pipeline, String name) {
-        Assert.assertEquals(pipeline.getProject().getName(), name);
-        Assert.assertTrue(pipeline.getProject().getReferenceFile().exists(), "reference not found");
-        Assert.assertTrue(pipeline.getProject().getIntervalList().exists(), "intervals not found");
-        Assert.assertTrue(pipeline.getProject().getRefseqTable().exists(), "refseq not found");
-        Assert.assertTrue(pipeline.getProject().getGenotypeDbsnp().exists(), "genotype dbsnp not found");
-        Assert.assertTrue(pipeline.getProject().getEvalDbsnp().exists(), "eval dbsnp not found");
-        Assert.assertEquals(pipeline.getSamples().size(), 1);
-        for (PipelineSample sample: pipeline.getSamples()) {
-            Assert.assertEquals(sample.getId(), PROJECT + "_" + SAMPLE);
-            Assert.assertTrue(sample.getBamFiles().get(PicardPipeline.PICARD_BAM_TYPE).exists(), "bam not found");
-            Assert.assertEquals(sample.getTags().get(PicardPipeline.PROJECT_TAG), PROJECT);
-            Assert.assertEquals(sample.getTags().get(PicardPipeline.SAMPLE_TAG), SAMPLE);
-        }
-    }
-
-    private File writeTsv(String project, String sample) throws IOException {
-        File tsv = BaseTest.createTempFile("pipeline", ".tsv");
-        FileUtils.writeLines(tsv, Collections.singletonList(project + "\t" + sample));
-        return tsv;
-    }
-
-    private File writeYaml(String projectName, String project, String sample) throws IOException {
-        File yaml = BaseTest.createTempFile("pipeline", ".yaml");
-        PipelineSample pipelineSample = new PipelineSample();
-        pipelineSample.getTags().put(PicardPipeline.PROJECT_TAG, project);
-        pipelineSample.getTags().put(PicardPipeline.SAMPLE_TAG, sample);
-        Pipeline pipeline = new Pipeline();
-        pipeline.getProject().setName(projectName);
-        pipeline.getSamples().add(pipelineSample);
-        YamlUtils.dump(pipeline, yaml);
-        return yaml;
-    }
-}
diff --git a/public/java/test/org/broadinstitute/sting/utils/broad/ReferenceDataUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/broad/ReferenceDataUnitTest.java
deleted file mode 100755
index e58ea3858..000000000
--- a/public/java/test/org/broadinstitute/sting/utils/broad/ReferenceDataUnitTest.java
+++ /dev/null
@@ -1,49 +0,0 @@
-package org.broadinstitute.sting.utils.broad;
-
-import org.broadinstitute.sting.BaseTest;
-import org.testng.Assert;
-import org.testng.annotations.Test;
-
-import java.io.File;
-
-public class ReferenceDataUnitTest {
-    @Test
-    public void testNames() {
-        Assert.assertEquals(ReferenceData.HG18.getName(), "hg18");
-        Assert.assertEquals(ReferenceData.HG19.getName(), "hg19");
-    }
-
-    @Test
-    public void testFilesExist() {
-        for (ReferenceData data: ReferenceData.values()) {
-            Assert.assertTrue(new File(data.getReference()).exists());
-            Assert.assertTrue(new File(data.getRefseq()).exists());
-            for (int version: data.getDbsnpVersions()) {
-                Assert.assertTrue(new File(data.getDbsnp(version)).exists());
-            }
-        }
-    }
-
-    @Test
-    public void testDbsnps() {
-        Assert.assertTrue(new File(ReferenceData.HG18.getDbsnp(129)).exists());
-        Assert.assertTrue(new File(ReferenceData.HG19.getDbsnp(129)).exists());
-        Assert.assertTrue(new File(ReferenceData.HG19.getDbsnp(132)).exists());
-        Assert.assertNull(ReferenceData.HG19.getDbsnp(130));
-    }
-
-    @Test
-    public void testDbsnpTypes() {
-        Assert.assertEquals(ReferenceData.HG18.getDbsnpType(129), "DBSNP");
-        Assert.assertEquals(ReferenceData.HG19.getDbsnpType(129), "VCF");
-        Assert.assertEquals(ReferenceData.HG19.getDbsnpType(132), "VCF");
-        Assert.assertNull(ReferenceData.HG19.getDbsnpType(130));
-    }
-
-    @Test
-    public void testGetByReference() {
-        Assert.assertEquals(ReferenceData.getByReference(BaseTest.hg18Reference), ReferenceData.HG18);
-        Assert.assertEquals(ReferenceData.getByReference(BaseTest.hg19Reference), ReferenceData.HG19);
-        Assert.assertEquals(ReferenceData.getByReference("none"), null);
-    }
-}
diff --git a/public/packages/Queue.xml b/public/packages/Queue.xml
index 347b24db3..58da4398e 100644
--- a/public/packages/Queue.xml
+++ b/public/packages/Queue.xml
@@ -33,7 +33,7 @@
             <package name="org.broadinstitute.sting.queue.**" />
 
             <!-- Pipeline + Utils -->
-            <package name="org.broadinstitute.sting.datasources.pipeline.**" />
+            <package name="org.broadinstitute.sting.pipeline.**" />
             <package name="org.broadinstitute.sting.utils.**" />
 
             <!-- Scala -->
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
index 6b87981ff..dc3cfd9d4 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
@@ -32,8 +32,6 @@ import java.util.Date
 import java.text.SimpleDateFormat
 import org.broadinstitute.sting.BaseTest
 import org.broadinstitute.sting.queue.QCommandLine
-import org.broadinstitute.sting.datasources.pipeline.{Pipeline, PipelineProject, PipelineSample}
-import org.broadinstitute.sting.utils.broad.PicardAggregationUtils
 import org.broadinstitute.sting.queue.util.{Logging, ProcessController}
 import java.io.{FileNotFoundException, File}
 import org.broadinstitute.sting.gatk.report.GATKReportParser
@@ -42,23 +40,6 @@ import org.broadinstitute.sting.queue.engine.CommandLinePluginManager
 
 object PipelineTest extends BaseTest with Logging {
 
-  case class K1gBam(squidId: String, sampleId: String, version: Int)
-
-  /** 1000G BAMs used for validation */
-  val k1gBams = List(
-    new K1gBam("C474", "NA19651", 2),
-    new K1gBam("C474", "NA19655", 2),
-    new K1gBam("C474", "NA19669", 2),
-    new K1gBam("C454", "NA19834", 2),
-    new K1gBam("C460", "HG01440", 2),
-    new K1gBam("C456", "NA12342", 2),
-    new K1gBam("C456", "NA12748", 2),
-    new K1gBam("C474", "NA19649", 2),
-    new K1gBam("C474", "NA19652", 2),
-    new K1gBam("C474", "NA19654", 2))
-
-  validateK1gBams()
-
   private val validationReportsDataLocation = "/humgen/gsa-hpprojects/GATK/validationreports/submitted/"
 
   val run = System.getProperty("pipeline.run") == "run"
@@ -92,49 +73,6 @@ object PipelineTest extends BaseTest with Logging {
    */
   private def tempDir(testName: String, jobRunner: String) = testDir(testName, jobRunner) + "temp/"
 
-  /**
-   * Creates a new pipeline from a project.
-   * @param project Pipeline project info.
-   * @param samples List of samples.
-   * @return a new pipeline project.
-   */
-  def createPipeline(project: PipelineProject, samples: List[PipelineSample]) = {
-    val pipeline = new Pipeline
-    pipeline.setProject(project)
-    pipeline.setSamples(samples)
-    pipeline
-  }
-
-  /**
-   * Creates a new pipeline project for hg19 with b37 132 dbsnp for genotyping, and b37 129 dbsnp for eval.
-   * @param projectName Name of the project.
-   * @param intervals The intervals file to use.
-   * @return a new pipeline project.
-   */
-  def createHg19Project(projectName: String, intervals: String) = {
-    val project = new PipelineProject
-    project.setName(projectName)
-    project.setReferenceFile(new File(BaseTest.hg19Reference))
-    project.setGenotypeDbsnp(new File(BaseTest.b37dbSNP132))
-    project.setEvalDbsnp(new File(BaseTest.b37dbSNP129))
-    project.setRefseqTable(new File(BaseTest.hg19Refseq))
-    project.setIntervalList(new File(intervals))
-    project
-  }
-
-  /**
-   * Creates a 1000G pipeline sample from one of the bams.
-   * @param idPrefix Text to prepend to the sample name.
-   * @param k1gBam bam to create the sample for.
-   * @return the created pipeline sample.
-   */
-  def createK1gSample(idPrefix: String, k1gBam: K1gBam) = {
-    val sample = new PipelineSample
-    sample.setId(idPrefix + "_" + k1gBam.sampleId)
-    sample.setBamFiles(Map("cleaned" -> getPicardBam(k1gBam)))
-    sample
-  }
-
   /**
    * Runs the pipelineTest.
    * @param pipelineTest test to run.
@@ -267,31 +205,6 @@ object PipelineTest extends BaseTest with Logging {
     }
   }
 
-  /**
-   * Throws an exception if any of the 1000G bams do not exist and warns if they are out of date.
-   */
-  private def validateK1gBams() {
-    var missingBams = List.empty[File]
-    for (k1gBam <- k1gBams) {
-      val latest = getLatestVersion(k1gBam)
-      val bam = getPicardBam(k1gBam)
-      if (k1gBam.version != latest)
-        logger.warn("1000G bam is not the latest version %d: %s".format(latest, k1gBam))
-      if (!bam.exists)
-        missingBams :+= bam
-    }
-    if (missingBams.size > 0) {
-      val nl = "%n".format()
-      throw new FileNotFoundException("The following 1000G bam files are missing.%n%s".format(missingBams.mkString(nl)))
-    }
-  }
-
-  private def getPicardBam(k1gBam: K1gBam): File =
-    new File(PicardAggregationUtils.getSampleBam(k1gBam.squidId, k1gBam.sampleId, k1gBam.version))
-
-  private def getLatestVersion(k1gBam: K1gBam): Int =
-    PicardAggregationUtils.getLatestVersion(k1gBam.squidId, k1gBam.sampleId, k1gBam.version)
-
   private var runningCommandLines = Set.empty[QCommandLine]
 
   Runtime.getRuntime.addShutdownHook(new Thread {