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Curiously, it seems I never set the default base quality used by the Genotyper to 10. It's done now. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2546 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-01-08 06:02:01 +00:00
parent b468369dfa
commit d5ab002449
2 changed files with 20 additions and 20 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
View File

@ -73,7 +73,7 @@ public class UnifiedArgumentCollection {
public double CONFIDENCE_THRESHOLD = 0.0;
@Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
public int MIN_BASE_QUALTY_SCORE = 20;
public int MIN_BASE_QUALTY_SCORE = 10;
@Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false)
public int MIN_MAPPING_QUALTY_SCORE = 10;

38
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("706efd396f3ac5e3addff73c15d1ec87"));
Arrays.asList("b7ea2739f9190ea6c5c63ffd1150454e"));
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("917d9ede2b2bccbcc41c6b7534788fa2"));
Arrays.asList("b200b56b0f6363105b23417f459ec4dc"));
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("48b3719bf39705983876276b8da2642f"));
Arrays.asList("1fc421c8e5ccba7ba2f803fc17c27565"));
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("057493e22a64cf5c78619707464cedbe"));
Arrays.asList("0078a4e6611cbfc7225f52209b87c4aa"));
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("05f32f8ba686260b79c98c661a01e8f8"));
Arrays.asList("9c862cf36124710648d6d8b83882c603"));
executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
}
@ -72,7 +72,7 @@ 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("5fcc0ecff04d408d33ce5fdc0a8d8b89"));
Arrays.asList("4f6aeda8903be49344353b79ee7763b4"));
executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
}
@ -85,7 +85,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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("b0e221e54f8ff9c6355654510acb7153"));
Arrays.asList("dbaff01edcfc8d83efa937f5887b26c2"));
executeTest("test parallelization", spec);
}
@ -98,11 +98,11 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-genotype", "d82b53aad30005330203a7ca07ce83d5" );
e.put( "-all_bases", "563566eaa2c621e88080149512d368b6" );
e.put( "-genotype", "c6abe711dade515e72b671d7e0d6e724" );
e.put( "-all_bases", "d9705e4c89f333f3fa6e771716db57e4" );
e.put( "--min_base_quality_score 26", "015509aca82954b89d7dc83134f2103e" );
e.put( "--min_mapping_quality_score 26", "ba7fe92be077750225c762981ead4b0d" );
e.put( "--max_mismatches_in_40bp_window 5", "abecda3de7b195d6d0f7ff97bc624b5f" );
e.put( "--min_mapping_quality_score 26", "a3926d2d24f9b4b4d772243a50ebdd59" );
e.put( "--max_mismatches_in_40bp_window 5", "ab592c8d0996d9bc4bb6685eaf874883" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -116,7 +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("c434515cae99d2da5a353f0b0866af81"));
Arrays.asList("15af52b80e2be8e8d2d489c3f86bdadc"));
executeTest("testConfidence", spec);
}
@ -129,8 +129,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOtherFormat() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "GLF", "2dabd6313cbf65564933187511bf823e" );
e.put( "GELI_BINARY", "e0af9777893c4b872b9ad867f0a2758c" );
e.put( "GLF", "cc1782d734e0a02fef00900a6db0e550" );
e.put( "GELI_BINARY", "764a0fed1b3cf089230fd91f3be9c2df" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -152,8 +152,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity() {
HashMap<Double, String> e = new HashMap<Double, String>();
e.put( 0.01, "0556dc160a18eeaf1a7303d5c1e1ce46" );
e.put( 1.0 / 1850, "0556dc160a18eeaf1a7303d5c1e1ce46" );
e.put( 0.01, "ee390f91867e8729b96220115e56ddb3" );
e.put( 1.0 / 1850, "f96ad0ed71449bdb16b0c5561303a05a" );
for ( Map.Entry<Double, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -172,8 +172,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOtherBaseCallModel() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "one_state", "78c4cfdd9ef21650709de5355178449a" );
e.put( "three_state", "8ae5cebc06d520b1277b2f71265dd7e0" );
e.put( "one_state", "bcc983210b576d9fd228a67c5b9f372a" );
e.put( "three_state", "2db3a5f3d46e13e2f44c34fbb7e7936f" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -200,7 +200,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -gm JOINT_ESTIMATE" +
" -vf GELI",
1,
Arrays.asList("1eabfec6a377992edb847d84608ab562"));
Arrays.asList("f09ac61858c2633e5d1326fcf098b36d"));
executeTest(String.format("testMultiTechnologies"), spec);
}