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Rank sum test annotations are the Z-scores from the test instead of the p-value. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5707 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-04-28 14:35:00 +00:00
parent 45081c32d7
commit b7334dcc1e
6 changed files with 34 additions and 42 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
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@ -12,7 +12,7 @@ import java.util.Arrays;
public class BaseQualityRankSumTest extends RankSumTest {
public List<String> getKeyNames() { return Arrays.asList("BaseQRankSum"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseQRankSum", 1, VCFHeaderLineType.Float, "Phred-scaled p-value From Wilcoxon Rank Sum Test of Alt Vs. Ref base qualities")); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseQRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities")); }
protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List<Integer> refQuals, List<Integer> altQuals) {
for ( final PileupElement p : pileup ) {

2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
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@ -13,7 +13,7 @@ public class MappingQualityRankSumTest extends RankSumTest {
public List<String> getKeyNames() { return Arrays.asList("MQRankSum"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("MQRankSum", 1, VCFHeaderLineType.Float, "Phred-scaled p-value From Wilcoxon Rank Sum Test of Alt Vs. Ref read mapping qualities")); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("MQRankSum", 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities")); }
protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List<Integer> refQuals, List<Integer> altQuals) {
for ( final PileupElement p : pileup ) {

10
java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
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@ -18,8 +18,6 @@ import java.util.HashMap;
public abstract class RankSumTest implements InfoFieldAnnotation, StandardAnnotation {
private static final double minPValue = 1e-20;
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;
@ -52,15 +50,9 @@ public abstract class RankSumTest implements InfoFieldAnnotation, StandardAnnota
// we are testing that set1 (the alt bases) have lower quality scores than set2 (the ref bases)
final Pair<Double,Double> testResults = mannWhitneyU.runOneSidedTest( MannWhitneyU.USet.SET1 );
double pvalue = testResults.second;
// deal with precision issues
if ( pvalue < minPValue ) {
pvalue = minPValue;
}
final Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.3f", Math.abs(QualityUtils.phredScaleErrorRate(pvalue))));
map.put(getKeyNames().get(0), String.format("%.3f", testResults.first));
return map;
}

2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
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@ -19,7 +19,7 @@ public class ReadPosRankSumTest extends RankSumTest {
public List<String> getKeyNames() { return Arrays.asList("ReadPosRankSum"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ReadPosRankSum", 1, VCFHeaderLineType.Float, "Phred-scaled p-value From Wilcoxon Rank Sum Test of Alt Vs. Ref read position bias")); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ReadPosRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias")); }
protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List<Integer> refQuals, List<Integer> altQuals) {
for ( final PileupElement p : pileup ) {

18
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("7e6dc39a191851f41d23753c4cca37a3"));
Arrays.asList("11fab4bbd26e0428e6d7b53284a34388"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("21f01de76f113627c1fa60d7954df871"));
Arrays.asList("4fb98442f2c09247fab296872abb5655"));
executeTest("test file has annotations, asking for annotations, #2", spec);
}
@ -63,7 +63,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("e5fccc9d2c8f21ab494aa2f878a5f197"));
Arrays.asList("4bcc71f014def02d0fe9237176cc99af"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}
@ -71,7 +71,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("76348339e6dd750308647d8c126c6f4c"));
Arrays.asList("c92e614ec796a5b39c5fdcc426410a9b"));
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
}
@ -79,7 +79,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testOverwritingHeader() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
Arrays.asList("e82ea45f1eef16b6ebf7def2171ee613"));
Arrays.asList("6c0d9d61f09d6b9036cdadf3f86f5e66"));
executeTest("test overwriting header", spec);
}
@ -87,7 +87,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoReads() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("426c0f2f8b94bdb50736519769a11355"));
Arrays.asList("019d6b1bb7b367759fc42fbdb14b8bf7"));
executeTest("not passing it any reads", spec);
}
@ -95,7 +95,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testDBTagWithDbsnp() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("f11c43c69e6aca81d7ec98d7ac39e5f6"));
Arrays.asList("92a29447f222eadb549dc05ddd11b45e"));
executeTest("getting DB tag with dbSNP", spec);
}
@ -103,7 +103,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testDBTagWithHapMap() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("921ff533873c37acd3849f56e41ebeec"));
Arrays.asList("067dde55de98a631225e0e084f0fcc1a"));
executeTest("getting DB tag with HM3", spec);
}
@ -111,7 +111,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testUsingExpression() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1,
Arrays.asList("8ea6f267094ab334ec0415a9177e2588"));
Arrays.asList("e55b457426d6ba7f8ccea085c23c1350"));
executeTest("using expression", spec);
}

42
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -27,13 +27,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("02481347a19d80e09538f2f6aa1be74a"));
Arrays.asList("a1add49e71306d72252ee3af3c40d2da"));
executeTest("test MultiSample Pilot1", spec);
}
@Test
public void testMultiSamplePilot2AndRecallingWithAlleles() {
String md5 = "d50bc17991d0dfd03ab2810a1cfeec85";
String md5 = "87a99063152ca935a1bec87ef19e0dad";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1,
@ -52,12 +52,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testWithAllelesPassedIn() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("bcb02e2a969edfbd290b9ec22f1a5884"));
Arrays.asList("a2584e8f92efa056cd8a09814476f883"));
executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("f1ff29ac1c79c76fcb6c290b39bc3a18"));
Arrays.asList("0d15caf026c74bf859900e717b7fe996"));
executeTest("test MultiSample Pilot2 with alleles passed in", spec2);
}
@ -65,7 +65,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -glm SNP -L 1:10,000,000-10,100,000", 1,
Arrays.asList("a7f59c32f63e8ca4c3ffe468c51fbaa2"));
Arrays.asList("2241d97972b72233cb7b4c565739698e"));
executeTest("test SingleSample Pilot2", spec);
}
@ -75,7 +75,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "211e4ed67cd7bd3501555d829548da48";
private final static String COMPRESSED_OUTPUT_MD5 = "64fd80527aa1b00fbbb4a77f1d5df48c";
@Test
public void testCompressedOutput() {
@ -136,9 +136,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testCallingParameters() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "--min_base_quality_score 26", "e74b0f3c3977f383645e82ae76034932" );
e.put( "--min_mapping_quality_score 26", "5f08d9e052bdb04a2a5ee78db349dde9" );
e.put( "--p_nonref_model GRID_SEARCH", "2f1350f76a571d28cd06e59ea6dffe4b" );
e.put( "--min_base_quality_score 26", "f91280e3c12646207b3d06f9a563699b" );
e.put( "--min_mapping_quality_score 26", "6f9e99469ec5f5ef333a5075e8149674" );
e.put( "--p_nonref_model GRID_SEARCH", "430cfe737affe6b179725e1eb0b95655" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -151,9 +151,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-sites_only", "63b76c4d26edf8cbb5bd91dafc81fee1" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "5bf0268945d953377ea3a811b20ff1bc" );
e.put( "--output_mode EMIT_ALL_SITES", "78eeff5b2277877954e4985934077d3f" );
e.put( "-sites_only", "81e01f685e98d8f18fa288beb1246881" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "3916157145aea448a38e4f12a0c381ae" );
e.put( "--output_mode EMIT_ALL_SITES", "7652e2362e7fc038bc0f41a03df5d9f4" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -167,12 +167,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
Arrays.asList("5f08d9e052bdb04a2a5ee78db349dde9"));
Arrays.asList("6f9e99469ec5f5ef333a5075e8149674"));
executeTest("test confidence 1", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
Arrays.asList("0d0bbfd08d1ce35ec1c007ba0f8dfe37"));
Arrays.asList("c2020de023bb3d731e17ed97aaa85c3d"));
executeTest("test confidence 2", spec2);
}
@ -184,8 +184,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity() {
HashMap<Double, String> e = new HashMap<Double, String>();
e.put( 0.01, "4fb6e66895bbaa9a3b9af91c985a2782" );
e.put( 1.0 / 1850, "1397d29d924e74f43de466927a9f7915" );
e.put( 0.01, "a56d3790bb2e18cec5a3099079431f19" );
e.put( 1.0 / 1850, "119dff78b9f3b415ef3ed9d1bc46dd04" );
for ( Map.Entry<Double, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -209,7 +209,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("b44ddfbeb9fc413e44194799b3e3bbf8"));
Arrays.asList("cd84c86ed02e4b052b96f76270ffd7fc"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -228,7 +228,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("164e25d61ef562ae863871d4ec7cb387"));
Arrays.asList("9b71db6bebce80022c8fde5db09de65f"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -248,7 +248,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -glm INDEL" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("08b63c534a7e129e53cdd1527d51be5c"));
Arrays.asList("84bc209f38d60f325f1a8b6292a82c82"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -263,7 +263,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -glm INDEL -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("b6546f6e8f092b3c39cffec22aa47bcb"));
Arrays.asList("f536ca23cb86b14fc20e453859dafc01"));
executeTest(String.format("test indel caller in SLX witn low min allele count"), spec);
}
@ -277,7 +277,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -glm INDEL" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("1d1ddad622dbee7e74550b5bb9d0928f"));
Arrays.asList("e9b4fef2cdfa4c4657f0df53309131b6"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}