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Moving VQSR v2 to core. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5740 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-05-03 20:20:06 +00:00
parent 44a717f63a
commit 23cd3a7a5d
14 changed files with 40 additions and 165 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java → java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/GaussianMixtureModel.java → java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import Jama.Matrix;
import cern.jet.random.Normal;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/MultivariateGaussian.java → java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import Jama.Matrix;
import org.apache.commons.math.special.Gamma;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrainingSet.java → java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.Tags;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/Tranche.java → java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrancheManager.java → java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java → java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.apache.log4j.Logger;
import org.broad.tribble.util.variantcontext.VariantContext;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantDataManager.java → java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import cern.jet.random.Normal;
import org.apache.log4j.Logger;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantDatum.java → java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.utils.GenomeLoc;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java → java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.commandline.Argument;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java → java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.commandline.Argument;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java → java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.apache.log4j.Logger;

108
java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
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@ -1,12 +1,10 @@
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test;
import org.testng.annotations.DataProvider;
import java.util.*;
import java.io.File;
public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
static HashMap<String, String> clusterFiles = new HashMap<String, String>();
@ -15,111 +13,61 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
private static class VRTest {
String inVCF;
String clusterMD5;
String tranchesMD5;
String recalVCFMD5;
String recalMD5;
String cutVCFMD5;
public VRTest(String inVCF, String clusterMD5, String tranchesMD5, String recalVCFMD5, String cutVCFMD5) {
public VRTest(String inVCF, String tranchesMD5, String recalMD5, String cutVCFMD5) {
this.inVCF = validationDataLocation + inVCF;
this.clusterMD5 = clusterMD5;
this.tranchesMD5 = tranchesMD5;
this.recalVCFMD5 = recalVCFMD5;
this.recalMD5 = recalMD5;
this.cutVCFMD5 = cutVCFMD5;
}
}
VRTest yriTrio = new VRTest("yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf",
"f65c27ee40053adc72dd0bfbb628e4d7", // cluster file
"dce581b880ffb6ea39cbada1ecc95915", // tranches
"c3e8a2f43656eab7d847dbf850f844a6", // recalVCF
"50f752a72643db9ad0aa94b3fc4e23d6"); // cut VCF
VRTest lowPass = new VRTest("lowpass.N3.chr1.raw.vcf",
"bda8f17cfc19d23e7e51f99e547f4b3d", // cluster file
"66edae83c50f4e8601fef7fafba774af", // tranches
"0123537e373657386068a534c0f5c91b", // recalVCF
"2172368e8585841e5ad96c95d0827c4b"); // cut VCF
VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
"920b12d7765eb4f6f4a1bab045679b31", // tranches
"41bbc5f07c8a9573d5bb638f01808bba", // recal file
"d9aa7a0f8fb886df4394f1636605adca"); // cut VCF
@DataProvider(name = "VRTest")
public Object[][] createData1() {
return new Object[][]{ {yriTrio}, {lowPass} };
return new Object[][]{ {lowPass} };
//return new Object[][]{ {yriTrio}, {lowPass} }; // Add hg19 chr20 trio calls here
}
@Test(dataProvider = "VRTest", enabled = true)
public void testGenerateVariantClusters(VRTest params) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -NO_HEADER" +
" --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -B:hapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/sites_r27_nr.b36_fwd.vcf" +
" -weightDBSNP 1.0 -weightHapMap 1.0" +
" -T GenerateVariantClusters" +
" -B:input,VCF " + params.inVCF +
" -L 1:50,000,000-200,000,000" +
" -qual 50.0" +
" --ignore_filter GATK_STANDARD" +
" -an QD -an MQ -an SB" +
" -clusterFile %s",
Arrays.asList(params.clusterMD5));
executeTest("testGenerateVariantClusters-"+params.inVCF, spec).getFirst();
}
@Test(dataProvider = "VRTest",dependsOnMethods="testGenerateVariantClusters")
@Test(dataProvider = "VRTest")
public void testVariantRecalibrator(VRTest params) {
//System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile);
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -NO_HEADER" +
" --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -B:hapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/sites_r27_nr.b36_fwd.vcf" +
" -B:truthHapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/sites_r27_nr.b36_fwd.vcf" +
"-R " + b37KGReference +
" -B:dbsnp,VCF,known=true,training=false,truth=false,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" +
" -B:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" +
" -B:omni,VCF,known=false,training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" +
" -T VariantRecalibrator" +
" -B:input,VCF " + params.inVCF +
" -L 1:20,000,000-100,000,000" +
" --ignore_filter GATK_STANDARD" +
" --ignore_filter HARD_TO_VALIDATE" +
" -clusterFile " + getFileForMD5(params.clusterMD5) +
" -sm TRUTH_SENSITIVITY" +
" -o %s" +
" -L 20:1,000,000-40,000,000" +
" -an QD -an HaplotypeScore -an HRun" +
" -percentBad 0.07" +
" --trustAllPolymorphic" + // for speed
" -recalFile %s" +
" -tranchesFile %s",
Arrays.asList(params.recalVCFMD5, params.tranchesMD5));
Arrays.asList(params.recalMD5, params.tranchesMD5));
executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst();
}
@Test(dataProvider = "VRTest",dependsOnMethods="testVariantRecalibrator")
public void testApplyVariantCuts(VRTest params) {
public void testApplyRecalibration(VRTest params) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
"-R " + b37KGReference +
" -T ApplyRecalibration" +
" -L 20:12,000,000-30,000,000" +
" -NO_HEADER" +
" --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -T ApplyVariantCuts" +
" -L 1:20,000,000-100,000,000" +
" -B:input,VCF " + getFileForMD5(params.recalVCFMD5) +
" -B:input,VCF " + params.inVCF +
" -o %s" +
" -tranchesFile " + getFileForMD5(params.tranchesMD5),
" -tranchesFile " + getFileForMD5(params.tranchesMD5) +
" -recalFile " + getFileForMD5(params.recalMD5),
Arrays.asList(params.cutVCFMD5));
executeTest("testApplyVariantCuts-"+params.inVCF, spec);
}
@Test()
public void testFailWithBadAnnotation() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -NO_HEADER" +
" --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -B:hapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/sites_r27_nr.b36_fwd.vcf" +
" -weightDBSNP 0.2 -weightHapMap 1.0" +
" -T GenerateVariantClusters" +
" -B:input,VCF " + lowPass.inVCF +
" -L 1:50,000,000-200,000,000" +
" -qual 50.0" +
" --ignore_filter GATK_STANDARD" +
" -an QD -an HRun -an ThisAnnotationIsBAD" + // There is a bad annotation here
" -clusterFile %s",
1, // just one output file
UserException.MalformedFile.class);
executeTest("testFailWithBadAnnotation", spec);
executeTest("testApplyRecalibration-"+params.inVCF, spec);
}
}

73
java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java
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@ -1,73 +0,0 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import org.testng.annotations.DataProvider;
import java.util.*;
public class VariantRecalibrationWalkersV2IntegrationTest extends WalkerTest {
static HashMap<String, String> clusterFiles = new HashMap<String, String>();
static HashMap<String, String> tranchesFiles = new HashMap<String, String>();
static HashMap<String, String> inputVCFFiles = new HashMap<String, String>();
private static class VRTest {
String inVCF;
String tranchesMD5;
String recalMD5;
String cutVCFMD5;
public VRTest(String inVCF, String tranchesMD5, String recalMD5, String cutVCFMD5) {
this.inVCF = validationDataLocation + inVCF;
this.tranchesMD5 = tranchesMD5;
this.recalMD5 = recalMD5;
this.cutVCFMD5 = cutVCFMD5;
}
}
VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
"920b12d7765eb4f6f4a1bab045679b31", // tranches
"41bbc5f07c8a9573d5bb638f01808bba", // recal file
"d9aa7a0f8fb886df4394f1636605adca"); // cut VCF
@DataProvider(name = "VRTest")
public Object[][] createData1() {
return new Object[][]{ {lowPass} };
//return new Object[][]{ {yriTrio}, {lowPass} }; // Add hg19 chr20 trio calls here
}
@Test(dataProvider = "VRTest")
public void testVariantRecalibrator(VRTest params) {
//System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile);
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b37KGReference +
" -B:dbsnp,VCF,known=true,training=false,truth=false,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" +
" -B:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" +
" -B:omni,VCF,known=false,training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" +
" -T VariantRecalibrator" +
" -B:input,VCF " + params.inVCF +
" -L 20:1,000,000-40,000,000" +
" -an QD -an HaplotypeScore -an HRun" +
" -percentBad 0.07" +
" --trustAllPolymorphic" + // for speed
" -recalFile %s" +
" -tranchesFile %s",
Arrays.asList(params.recalMD5, params.tranchesMD5));
executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst();
}
@Test(dataProvider = "VRTest",dependsOnMethods="testVariantRecalibrator")
public void testApplyRecalibration(VRTest params) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b37KGReference +
" -T ApplyRecalibration" +
" -L 20:12,000,000-30,000,000" +
" -NO_HEADER" +
" -B:input,VCF " + params.inVCF +
" -o %s" +
" -tranchesFile " + getFileForMD5(params.tranchesMD5) +
" -recalFile " + getFileForMD5(params.recalMD5),
Arrays.asList(params.cutVCFMD5));
executeTest("testApplyRecalibration-"+params.inVCF, spec);
}
}