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1. Variation is now passed to VariantAnnotator along with the List of Genotypes so non-genotype calls has access to all relevant info. 

2. Killed OnOffGenoype
3. SpanningDeletions is now SpanningDeletionFraction



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2151 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-11-24 21:47:20 +00:00
parent e05cb346f3
commit 3484f652e7
17 changed files with 41 additions and 173 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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@ -10,7 +10,7 @@ import java.util.ArrayList;
public class AlleleBalance extends StandardVariantAnnotation {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes) {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
if ( genotypes.size() == 0 )
return null;

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
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@ -4,13 +4,14 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import java.util.List;
public class DepthOfCoverage extends StandardVariantAnnotation {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes) {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
int depth = pileup.getReads().size();
return new Pair<String, String>("DoC", String.format("%d", depth));
}

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import net.sf.samtools.SAMRecord;
import cern.jet.math.Arithmetic;
@ -13,7 +14,7 @@ import java.util.List;
public class FisherStrand extends StandardVariantAnnotation {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes) {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
// this test doesn't make sense for homs
Genotype genotype = VariantAnnotator.getFirstHetVariant(genotypes);

14
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
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@ -5,25 +5,19 @@ import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import java.util.List;
public class HomopolymerRun extends StandardVariantAnnotation {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes) {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
Genotype genotype = VariantAnnotator.getFirstVariant(ref.getBase(), genotypes);
if ( genotype == null )
if ( !variation.isBiallelic() || !variation.isSNP() )
return null;
final String genotypeStr = genotype.getBases().toUpperCase();
if ( genotypeStr.length() != 2 )
return null;
char altAllele = (genotypeStr.charAt(0) != ref.getBase() ? genotypeStr.charAt(0) : genotypeStr.charAt(1));
int run = computeHomopolymerRun(altAllele, ref);
int run = computeHomopolymerRun(variation.getAlternativeBaseForSNP(), ref);
return new Pair<String, String>("HomopolymerRun", String.format("%d", run));
}

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
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@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import net.sf.samtools.SAMRecord;
import java.util.List;
@ -11,7 +12,7 @@ import java.util.List;
public class MappingQualityZero extends StandardVariantAnnotation {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes) {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
List<SAMRecord> reads = pileup.getReads();
int MQ0Count = 0;
for (int i=0; i < reads.size(); i++) {

135
java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java
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@ -1,135 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.ReadBacked;
import org.broadinstitute.sting.utils.genotype.PosteriorsBacked;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import java.util.List;
import java.util.ArrayList;
public class OnOffGenotype extends StandardVariantAnnotation {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes) {
if ( genotypes.size() == 0 )
return null;
double ratio;
Genotype g = genotypes.get(0);
if ( g instanceof ReadBacked && g instanceof PosteriorsBacked) {
Pair<Double, Integer> weightedBalance = computeWeightedBalance(ref.getBase(), genotypes, pileup);
if ( weightedBalance.second == 0 )
return null;
ratio = weightedBalance.first;
} else {
Genotype genotype = VariantAnnotator.getFirstVariant(ref.getBase(), genotypes);
if ( genotype == null )
return null;
final String genotypeStr = genotype.getBases().toUpperCase();
if ( genotypeStr.length() != 2 )
return null;
final String bases = pileup.getBasesAsString().toUpperCase();
if ( bases.length() == 0 )
return null;
ratio = computeSingleBalance(genotypeStr, bases);
}
return new Pair<String, String>("OnOffGenotype", String.format("%.2f", ratio));
}
private double computeSingleBalance(final String genotypeStr, final String bases) {
int on = 0, off = 0;
for ( char base : BaseUtils.BASES ) {
int count = BasicPileup.countBase(base, bases);
if ( Utils.countOccurrences(base, genotypeStr) > 0 )
on += count;
else
off += count;
}
double ratio = (double)on / (double)(on + off);
return ratio;
}
private Pair<Double, Integer> computeWeightedBalance(char ref, List<Genotype> genotypes, ReadBackedPileup pileup) {
ArrayList<Double> onOffBalances = new ArrayList<Double>();
ArrayList<Double> weights = new ArrayList<Double>();
// accumulate ratios and weights
for ( Genotype g : genotypes ) {
if ( !(g instanceof ReadBacked) || !(g instanceof PosteriorsBacked) )
continue;
final String genotypeStr = g.getBases().toUpperCase();
if ( genotypeStr.length() != 2 )
continue;
DiploidGenotype bestGenotype = DiploidGenotype.unorderedValueOf(genotypeStr);
// we care only about non-ref calls
if ( bestGenotype.isHomRef(ref) )
continue;
char a = genotypeStr.charAt(0);
char b = genotypeStr.charAt(1);
// get the base counts at this pileup (minus deletions)
ReadBackedPileup myPileup = ((ReadBacked)g).getPileup();
// if the pileup is null, we'll just have to use the full pileup (it's better than nothing)
if ( myPileup == null )
myPileup = pileup;
int[] counts = myPileup.getBasePileupAsCounts();
int onCount = counts[BaseUtils.simpleBaseToBaseIndex(a)];
if ( a != b )
onCount += counts[BaseUtils.simpleBaseToBaseIndex(b)];
int totalCount = 0;
for (int i = 0; i < counts.length; i++)
totalCount += counts[i];
// sanity check
if ( totalCount == 0 )
continue;
double[] posteriors = ((PosteriorsBacked)g).getPosteriors();
posteriors = MathUtils.normalizeFromLog10(posteriors);
double weight = posteriors[bestGenotype.ordinal()];
// sanity check
if ( MathUtils.compareDoubles(weight, 0.0) == 0 )
continue;
weights.add(weight);
onOffBalances.add((double)onCount / (double)totalCount);
}
double ratio = 0.0;
if ( weights.size() > 0 ) {
// normalize the weights
double sum = 0.0;
for (int i = 0; i < weights.size(); i++)
sum += weights.get(i);
for (int i = 0; i < weights.size(); i++)
weights.set(i, weights.get(i) / sum);
// calculate total weighted ratios
for (int i = 0; i < weights.size(); i++)
ratio += weights.get(i) * onOffBalances.get(i);
}
return new Pair<Double, Integer>(ratio, weights.size());
}
public boolean useZeroQualityReads() { return false; }
}

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/PrimaryBaseSecondaryBaseSymmetry.java
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@ -4,6 +4,7 @@ import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.apache.log4j.Logger;
@ -34,7 +35,7 @@ public class PrimaryBaseSecondaryBaseSymmetry implements VariantAnnotation{
public boolean useZeroQualityReads() { return USE_ZERO_QUALITY_READS; }
public Pair<String,String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes) {
public Pair<String,String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
Pair<Integer,Double> refSecondBasePair = getProportionOfReferenceSecondBasesThatSupportAlt(ref, pileup, genotypes);
Pair<Integer,Double> nonrefPrimaryBasePair = getProportionOfPrimaryNonrefBasesThatSupportAlt(ref, pileup, genotypes);
if ( refSecondBasePair == null || nonrefPrimaryBasePair == null ) {

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
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@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import net.sf.samtools.SAMRecord;
import java.util.List;
@ -12,7 +13,7 @@ import java.util.List;
public class RMSMappingQuality extends StandardVariantAnnotation {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes) {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
List<SAMRecord> reads = pileup.getReads();
int[] qualities = new int[reads.size()];
for (int i=0; i < reads.size(); i++)

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/ResidualQuality.java
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@ -4,6 +4,7 @@ import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import java.util.List;
@ -21,7 +22,7 @@ public class ResidualQuality implements VariantAnnotation{
public boolean useZeroQualityReads() { return true; } // for robustness
public Pair<String,String> annotate( ReferenceContext ref, ReadBackedPileup p, List<Genotype> genotypes) {
public Pair<String,String> annotate( ReferenceContext ref, ReadBackedPileup p, Variation variation, List<Genotype> genotypes) {
Character snp = getSNPChar(ref, genotypes);
if ( snp == null ) {

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
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@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import java.util.List;
@ -26,7 +27,7 @@ public class SecondBaseSkew implements VariantAnnotation{
public boolean useZeroQualityReads() { return USE_ZERO_QUALITY_READS; }
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes) {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
double chi_square;
Pair<Integer,Double> depthProp = getSecondaryPileupNonrefEstimator(pileup,genotypes);
if ( depthProp == null ) {

5
java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
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@ -4,19 +4,20 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import java.util.List;
public class SpanningDeletions extends StandardVariantAnnotation {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes) {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
int deletions = 0;
for (Integer offset : pileup.getOffsets() ) {
if ( offset == -1 )
deletions++;
}
return new Pair<String, String>("SpanningDeletions", String.format("%d", deletions));
return new Pair<String, String>("SpanningDeletionFraction", String.format("%.2f", (double)deletions/(double)pileup.getReads().size()));
}
public boolean useZeroQualityReads() { return false; }

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotation.java
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@ -4,12 +4,13 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import java.util.List;
public interface VariantAnnotation {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, List<Genotype> genotypes);
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes);
public boolean useZeroQualityReads();
}

10
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -169,7 +169,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
variant instanceof VariantBackedByGenotype ) {
final List<org.broadinstitute.sting.utils.genotype.Genotype> genotypes = ((VariantBackedByGenotype)variant).getGenotypes();
if ( genotypes != null )
annotations = getAnnotations(ref, context, genotypes, requestedAnnotations);
annotations = getAnnotations(ref, context, variant, genotypes, requestedAnnotations);
}
writeVCF(tracker, ref, context, variant, annotations);
@ -177,13 +177,13 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
return 1;
}
public static Map<String, String> getAnnotations(ReferenceContext ref, AlignmentContext context, List<Genotype> genotypes) {
public static Map<String, String> getAnnotations(ReferenceContext ref, AlignmentContext context, Variation variation, List<Genotype> genotypes) {
if ( standardAnnotations == null )
determineAllAnnotations();
return getAnnotations(ref, context, genotypes, standardAnnotations.values());
return getAnnotations(ref, context, variation, genotypes, standardAnnotations.values());
}
public static Map<String, String> getAnnotations(ReferenceContext ref, AlignmentContext context, List<Genotype> genotypes, Collection<VariantAnnotation> annotations) {
public static Map<String, String> getAnnotations(ReferenceContext ref, AlignmentContext context, Variation variation, List<Genotype> genotypes, Collection<VariantAnnotation> annotations) {
// set up the pileup for the full collection of reads at this position
ReadBackedPileup fullPileup = new ReadBackedPileup(ref.getBase(), context);
@ -208,7 +208,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
HashMap<String, String> results = new HashMap<String, String>();
for ( VariantAnnotation annotator : annotations) {
Pair<String, String> annot = annotator.annotate(ref, (annotator.useZeroQualityReads() ? fullPileup : MQ0freePileup), genotypes);
Pair<String, String> annot = annotator.annotate(ref, (annotator.useZeroQualityReads() ? fullPileup : MQ0freePileup), variation, genotypes);
if ( annot != null ) {
// System.out.println("Annotating: First="+annot.getFirst()+" Second="+annot.getSecond());
results.put(annot.first, annot.second);

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -175,7 +175,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<List<Genotype>, GenotypeL
// annotate the call, if possible
if ( call != null && call.second != null && call.second instanceof ArbitraryFieldsBacked ) {
Map<String, String> annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.first);
Map<String, String> annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.second, call.first);
((ArbitraryFieldsBacked)call.second).setFields(annotations);
}

2
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
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@ -124,7 +124,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
params.setLocations(locusdata.getLocation(), locusdata.getReference().charAt(0));
// if there is no genotype data, we'll also need to set an alternate allele
if ( locusdata.isSNP() && locusdata.isBiallelic() )
if ( locusdata.isBiallelic() && locusdata.isSNP() )
params.addAlternateBase(new VCFGenotypeEncoding(locusdata.getAlternateAlleleList().get(0)));
} else {
params.setLocations(genotypes.get(0).getLocation(), genotypes.get(0).getReference());

8
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -all -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("3b54731a929134410f167630ec434310"));
Arrays.asList("aa4fd832eab85123b97c7961c9c8402a"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -all -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("c713d6d6cf922eab4150737f51f13abc"));
Arrays.asList("1f757921997fb5db79e2c4a79082e6d1"));
executeTest("test file has annotations, asking for annotations, #2", spec);
}
@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -all -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("0feb1dd8aae945ce5f05c1156acadd3c"));
Arrays.asList("ad3945cab44444d3b1c0bd35307814f7"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}
@ -106,7 +106,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -all -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("b15b965af6d204cbb2926f59f68d987c"));
Arrays.asList("417917556d3a0f7da0eb3830e6b33c71"));
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
}

12
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -47,7 +47,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1PointEM() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
Arrays.asList("fbb3ae6e835df5cf9b99dae5bf1fa8e5"));
Arrays.asList("90072e7f935357695f8f48c40ff6e7a4"));
executeTest("testMultiSamplePilot1 - Point Estimate EM", spec);
}
@ -55,7 +55,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot2PointEM() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
Arrays.asList("98495e6f75a63558996ed45f7a1f062a"));
Arrays.asList("72bcbd0786bb94803d1ad867becf12e2"));
executeTest("testMultiSamplePilot2 - Point Estimate EM", spec);
}
@ -68,7 +68,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testPooled1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1,
Arrays.asList("80fcd214108b4f4145ae585e5f119460"));
Arrays.asList("cdbda4a455f11f75fa666e9317139f22"));
executeTest("testPooled1", spec);
}
@ -81,7 +81,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
Arrays.asList("e1a206a49982f7db5c3f4b65aa910b3a"));
Arrays.asList("415f4a276005cad7fea0a8fcc3b8c3b5"));
executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
}
@ -89,7 +89,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot2Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
Arrays.asList("7eb10aec21497da727eeb67bb5c5a743"));
Arrays.asList("8673c7dbe8dc4e93726706bd9276afc3"));
executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
}
@ -97,7 +97,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
Arrays.asList("0cd57b2b6272202db0eca45376fdb01d"));
Arrays.asList("3d9bcf0f5525014f06b68fa006ef3fa3"));
executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
}