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Removed the VCF "NS" annotation (which wasn't working for pooled calls anyways) since it's ambiguous and not useful. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2465 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-29 17:30:47 +00:00
parent e32174fbc4
commit 5fdf17fccb
5 changed files with 34 additions and 22 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -180,7 +180,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
// annotation (INFO) fields from UnifiedGenotyper
headerInfo.add(new VCFHeaderLine("INFO_NOTE", "\"All annotations in the INFO field are generated only from the FILTERED context used for calling variants\""));
headerInfo.add(new VCFInfoHeaderLine(VCFRecord.ALLELE_FREQUENCY_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Allele Frequency"));
headerInfo.add(new VCFInfoHeaderLine(VCFRecord.SAMPLE_NUMBER_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Number of Samples With Data"));
// no longer used: headerInfo.add(new VCFInfoHeaderLine(VCFRecord.SAMPLE_NUMBER_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Number of Samples With Data"));
if ( !UAC.NO_SLOD )
headerInfo.add(new VCFInfoHeaderLine(VCFRecord.STRAND_BIAS_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Strand Bias"));

7
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
View File

@ -131,7 +131,7 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
}
// info fields
Map<String, String> infoFields = getInfoFields((VCFVariationCall)locusdata, params);
Map<String, String> infoFields = getInfoFields((VCFVariationCall)locusdata);
// q-score
double qual = (locusdata == null) ? 0 : ((VCFVariationCall)locusdata).getConfidence();
@ -165,11 +165,10 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
* get the information fields of the VCF record, given the meta data and parameters
*
* @param locusdata the metadata associated with this multi sample call
* @param params the parameters
*
* @return a mapping of info field to value
*/
private static Map<String, String> getInfoFields(VCFVariationCall locusdata, VCFParameters params) {
private static Map<String, String> getInfoFields(VCFVariationCall locusdata) {
Map<String, String> infoFields = new HashMap<String, String>();
if ( locusdata != null ) {
if ( locusdata.getSLOD() != null )
@ -181,7 +180,7 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
infoFields.putAll(otherFields);
}
}
infoFields.put(VCFRecord.SAMPLE_NUMBER_KEY, String.valueOf(params.getGenotypesRecords().size()));
// no longer used: infoFields.put(VCFRecord.SAMPLE_NUMBER_KEY, String.valueOf(params.getGenotypesRecords().size()));
return infoFields;
}

2
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
View File

@ -171,7 +171,7 @@ public class VCFUtils {
Map<String, String> infoFields = new HashMap<String, String>();
infoFields.put(VCFRecord.DEPTH_KEY, String.format("%d", totalReadDepth));
infoFields.put(VCFRecord.SAMPLE_NUMBER_KEY, String.valueOf(params.getGenotypesRecords().size()));
// no longer used: infoFields.put(VCFRecord.SAMPLE_NUMBER_KEY, String.valueOf(params.getGenotypesRecords().size()));
// set the overall strand bias and allele frequency to be the average of all entries we've seen
if ( SLODsSeen > 0 )

8
java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java
View File

@ -14,7 +14,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
public void testSimpleVenn() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SimpleVenn", 1,
Arrays.asList("5c8e4757d2ce46bc50991a171f988327"));
Arrays.asList("f4c4b7430f0e293c27ce38cb89b9338b"));
executeTest("testSimpleVenn", spec);
}
@ -22,7 +22,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
public void testSNPConcordance() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SNPGenotypeConcordance:qscore=5", 1,
Arrays.asList("b4904813cdfd37f0a092aa6cadcd3f71"));
Arrays.asList("f754e046bc0fa3a4b3430061e412ef0d"));
executeTest("testSNPConcordance", spec);
}
@ -30,7 +30,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
public void testNWayVenn() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -B set3,VCF," + validationDataLocation + "CEU.sample.vcf -CT NWayVenn", 1,
Arrays.asList("cf915dc9762d6a44a7bdadc0d7eae9b8"));
Arrays.asList("0527ea8ec7de3a144bd0a56db80d62ba"));
executeTest("testNWayVenn", spec);
}
@ -38,7 +38,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
public void testMulti() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SimpleVenn -CT NWayVenn -CT SNPGenotypeConcordance:qscore=5", 1,
Arrays.asList("d046599a2fef386fa0ad5dfc9671c3a9"));
Arrays.asList("6fbe00cb68d2cdc59dfcb79024fd9893"));
executeTest("testMulti", spec);
}
}

37
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -22,7 +22,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1PointEM() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "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("caeb030b47503e9d79cf1e18b86e8bc9"));
Arrays.asList("94c6c400cbeae33fcd6fea3388fcf73a"));
executeTest("testMultiSamplePilot1 - Point Estimate EM", spec);
}
@ -30,7 +30,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot2PointEM() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "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("f87c182b694a7baeab886d8f75c91e28"));
Arrays.asList("ee14f4328fde95b35e3b1cb919c3712b"));
executeTest("testMultiSamplePilot2 - Point Estimate EM", spec);
}
@ -43,7 +43,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testPooled1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "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("acf8006174a460247fabbc650802c29b"));
Arrays.asList("68a4120d7dc9f1880f41311f095978ea"));
executeTest("testPooled1", spec);
}
@ -56,7 +56,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "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("92b32599938bc60d6d636b425c5e0a6c"));
Arrays.asList("4504dd9c77dc502e9acbe687063a82c7"));
executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
}
@ -64,7 +64,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot2Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "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("cc90c3dd5d30dd4ac0fceb748283ddb9"));
Arrays.asList("15fefcebedae65c1f0c94b8498bc647a"));
executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
}
@ -72,10 +72,23 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "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("d04c02cdbf1e1adbdf84540c861a64f7"));
Arrays.asList("d87b46694da0cc8b0ff82c1c69ee073f"));
executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing joint estimation model
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testParallelization() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,400,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 -nt 4", 1,
Arrays.asList("bcbdd0369a0621d40bbdd6ef4c13f057"));
executeTest("test parallelization", spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing parameters
@ -85,11 +98,11 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-genotype", "ce888ec4bdd85e24b1129198327ff315" );
e.put( "-all_bases", "95be4777a8f89f98d0a033fc3d75a3c1" );
e.put( "--min_base_quality_score 10", "390802b120cba6019af39d4775f504d1" );
e.put( "--min_mapping_quality_score 10", "f7fe79dace81157bc83c8e4d27e1ae40" );
e.put( "--max_mismatches_in_40bp_window 5", "0e7741a7a683a6d4d00876372bb70991" );
e.put( "-genotype", "990d3e9b63310f56bf781959763804ae" );
e.put( "-all_bases", "6f24401c4b82b270739d596077da8582" );
e.put( "--min_base_quality_score 10", "2a53a3889fe1c32b066228f749ab4790" );
e.put( "--min_mapping_quality_score 10", "224c962fc6178059ae36ed9a4d614d26" );
e.put( "--max_mismatches_in_40bp_window 5", "fa8dd3c00d36ca62a88b5ceeb50ee33b" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -103,7 +116,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10 ", 1,
Arrays.asList("c8c4a463ab23585d8373f3e8a7fbec22"));
Arrays.asList("13aad04333ef26eca6179221acf8abc0"));
executeTest("testConfidence", spec);
}