From b668d32cf1ca82222776d89215b2c01df4b1c774 Mon Sep 17 00:00:00 2001 From: ebanks Date: Sun, 3 Jan 2010 21:31:04 +0000 Subject: [PATCH] Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2494 348d0f76-0448-11de-a6fe-93d51630548a --- .../filters/MappingQualityReadFilter.java | 2 +- .../genotyper/UnifiedArgumentCollection.java | 12 +++--- .../UnifiedGenotyperIntegrationTest.java | 40 +++++++++---------- 3 files changed, 27 insertions(+), 27 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java index b9ad8a60b..77e4ebb30 100755 --- a/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java +++ b/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java @@ -38,7 +38,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; public class MappingQualityReadFilter implements SamRecordFilter { @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 = 30; + public int MIN_MAPPING_QUALTY_SCORE = 10; public boolean filterOut(SAMRecord rec) { return (rec.getMappingQuality() < MIN_MAPPING_QUALTY_SCORE); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 6fc1c3f97..cc70ff1db 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -72,6 +72,12 @@ public class UnifiedArgumentCollection { @Argument(fullName = "min_confidence_threshold", shortName = "confidence", doc = "The phred-scaled confidence threshold by which variants should be filtered", required = false) 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; + + @Argument(fullName = "max_mismatches_in_40bp_window", shortName = "mm40", doc = "Maximum number of mismatches within a 40 bp window (20bp on either side) around the target position for a read to be used for calling", required = false) + public int MAX_MISMATCHES = 3; + @Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]", required = false) public Double MAX_DELETION_FRACTION = 0.05; @@ -80,10 +86,4 @@ public class UnifiedArgumentCollection { @Argument(fullName = "min_allele_frequency", shortName = "min_freq", doc = "The minimum possible allele frequency in a population (advanced)", required = false) public double MINIMUM_ALLELE_FREQUENCY = 1e-8; - - @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; - - @Argument(fullName = "max_mismatches_in_40bp_window", shortName = "mm40", doc = "Maximum number of mismatches within a 40 bp window (20bp on either side) around the target position for a read to be used for calling", required = false) - public int MAX_MISMATCHES = 3; } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 2c5434397..d216ef53f 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -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("94c6c400cbeae33fcd6fea3388fcf73a")); + Arrays.asList("8acbb0879a7c9f35e7cf7d77a7cab850")); 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("ee14f4328fde95b35e3b1cb919c3712b")); + Arrays.asList("a5ec48e6695d9a5e7fcced7775baf6ff")); 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("68a4120d7dc9f1880f41311f095978ea")); + Arrays.asList("c20f370440ed55b0b6c38715985a850d")); 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("4504dd9c77dc502e9acbe687063a82c7")); + Arrays.asList("0a2df3fc9fc72a3ace46aab899275636")); 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("15fefcebedae65c1f0c94b8498bc647a")); + Arrays.asList("52249b69d5d984a8bdc0438e1f106dcb")); 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("d87b46694da0cc8b0ff82c1c69ee073f")); + Arrays.asList("172ca88b718f24fa0f2a3460b2dab33d")); 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("bcbdd0369a0621d40bbdd6ef4c13f057")); + Arrays.asList("d86d9148b1eee16da9a5bb57c929c0c9")); executeTest("test parallelization", spec); } @@ -98,11 +98,11 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testParameter() { HashMap e = new HashMap(); - 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" ); + e.put( "-genotype", "2a8b8d4da5ceed494e2210b15c2c3eb0" ); + e.put( "-all_bases", "69b20ce7fc18f78011ee02b48a8d69aa" ); + e.put( "--min_base_quality_score 26", "67175e0262e626d46aaf3bc8680cf888" ); + e.put( "--min_mapping_quality_score 26", "8edb24206529a7a344008280ab69cbb2" ); + e.put( "--max_mismatches_in_40bp_window 5", "870812ed23b2c656439dc1c8e6376f89" ); for ( Map.Entry 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("13aad04333ef26eca6179221acf8abc0")); + Arrays.asList("eb708a714a0ecbebed707f2d9684e165")); executeTest("testConfidence", spec); } @@ -129,8 +129,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOtherFormat() { HashMap e = new HashMap(); - e.put( "GLF", "8c72131dfb2b830efb9938a582672a3e" ); - e.put( "GELI_BINARY", "46162567eac3a5004f5f9b4c93d1b8d3" ); + e.put( "GLF", "2dabd6313cbf65564933187511bf823e" ); + e.put( "GELI_BINARY", "e0af9777893c4b872b9ad867f0a2758c" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -152,8 +152,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testHeterozyosity() { HashMap e = new HashMap(); - e.put( 0.01, "700e6426c4142c823f7ac1dde2aa19ea" ); - e.put( 1.0 / 1850, "e9e00bdb32ce63420988956c1a9b805f" ); + e.put( 0.01, "0556dc160a18eeaf1a7303d5c1e1ce46" ); + e.put( 1.0 / 1850, "0556dc160a18eeaf1a7303d5c1e1ce46" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -172,8 +172,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOtherBaseCallModel() { HashMap e = new HashMap(); - e.put( "one_state", "d69abadc3bf861d621017c0e41b87b0a" ); - e.put( "three_state", "ebcc76cc4579393f98aecb59bdc56507" ); + e.put( "one_state", "78c4cfdd9ef21650709de5355178449a" ); + e.put( "three_state", "8ae5cebc06d520b1277b2f71265dd7e0" ); for ( Map.Entry 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("64ffb4ef633ad4c2ff6afbc75450f743")); + Arrays.asList("1eabfec6a377992edb847d84608ab562")); executeTest(String.format("testMultiTechnologies"), spec); }