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Let's go back to having the SB/SLOD NOT computed by default. If you recall, it was only enabled by default because we thought we were going to use it when we made VQSR use random forests. But since we decided not to change VQSR, there's no reason to triple the computation for every variant site anymore.

This commit is contained in:
Eric Banks 2012-10-25 12:45:23 -04:00
parent 6dc7d872ec
commit e93ff3ea6e
5 changed files with 14 additions and 15 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -47,8 +47,8 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
/** /**
* Note that calculating the SLOD increases the runtime by an appreciable amount. * Note that calculating the SLOD increases the runtime by an appreciable amount.
*/ */
@Argument(fullName = "noSLOD", shortName = "nosl", doc = "If provided, we will not calculate the SLOD", required = false) @Argument(fullName = "computeSLOD", shortName = "slod", doc = "If provided, we will calculate the SLOD (SB annotation)", required = false)
public boolean NO_SLOD = false; public boolean COMPUTE_SLOD = false;
/** /**
* Depending on the value of the --max_alternate_alleles argument, we may genotype only a fraction of the alleles being sent on for genotyping. * Depending on the value of the --max_alternate_alleles argument, we may genotype only a fraction of the alleles being sent on for genotyping.
@ -204,7 +204,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
this.GLmodel = uac.GLmodel; this.GLmodel = uac.GLmodel;
this.AFmodel = uac.AFmodel; this.AFmodel = uac.AFmodel;
this.PCR_error = uac.PCR_error; this.PCR_error = uac.PCR_error;
this.NO_SLOD = uac.NO_SLOD; this.COMPUTE_SLOD = uac.COMPUTE_SLOD;
this.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED = uac.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED; this.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED = uac.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED;
this.MIN_BASE_QUALTY_SCORE = uac.MIN_BASE_QUALTY_SCORE; this.MIN_BASE_QUALTY_SCORE = uac.MIN_BASE_QUALTY_SCORE;
this.MAX_DELETION_FRACTION = uac.MAX_DELETION_FRACTION; this.MAX_DELETION_FRACTION = uac.MAX_DELETION_FRACTION;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -290,7 +290,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions()); headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions());
// annotation (INFO) fields from UnifiedGenotyper // annotation (INFO) fields from UnifiedGenotyper
if ( !UAC.NO_SLOD ) if ( UAC.COMPUTE_SLOD )
VCFStandardHeaderLines.addStandardInfoLines(headerInfo, true, VCFConstants.STRAND_BIAS_KEY); VCFStandardHeaderLines.addStandardInfoLines(headerInfo, true, VCFConstants.STRAND_BIAS_KEY);
if ( UAC.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED ) if ( UAC.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -451,7 +451,7 @@ public class UnifiedGenotyperEngine {
attributes.put(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, MLEfrequencies); attributes.put(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, MLEfrequencies);
} }
if ( !UAC.NO_SLOD && !limitedContext && !bestGuessIsRef ) { if ( UAC.COMPUTE_SLOD && !limitedContext && !bestGuessIsRef ) {
//final boolean DEBUG_SLOD = false; //final boolean DEBUG_SLOD = false;
// the overall lod // the overall lod

1
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -459,7 +459,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH; UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH;
UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES; UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES; UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
UAC.NO_SLOD = true;
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY); UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
headerLines.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null)); headerLines.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null));
} }

18
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -16,9 +16,9 @@ import java.util.List;
public class UnifiedGenotyperIntegrationTest extends WalkerTest { public class UnifiedGenotyperIntegrationTest extends WalkerTest {
private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129; private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl --no_cmdline_in_header -glm INDEL -mbq 20 -minIndelFrac 0.0 --dbsnp " + b36dbSNP129; private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm INDEL -mbq 20 -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132; private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132;
private final static String baseCommandNoCmdLineHeaderStdout = "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam"; private final static String baseCommandNoCmdLineHeaderStdout = "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam";
// -------------------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------------------
@ -61,7 +61,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test @Test
public void testMultipleSNPAlleles() { public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1, "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
Arrays.asList("543f68e42034bf44cfb24da8c9204320")); Arrays.asList("543f68e42034bf44cfb24da8c9204320"));
executeTest("test Multiple SNP alleles", spec); executeTest("test Multiple SNP alleles", spec);
} }
@ -69,7 +69,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test @Test
public void testBadRead() { public void testBadRead() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1, "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
Arrays.asList("d915535c1458733f09f82670092fcab6")); Arrays.asList("d915535c1458733f09f82670092fcab6"));
executeTest("test bad read", spec); executeTest("test bad read", spec);
} }
@ -77,7 +77,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test @Test
public void testReverseTrim() { public void testReverseTrim() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1, "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
Arrays.asList("5ce03dd9ca2d9324c1d4a9d64389beb5")); Arrays.asList("5ce03dd9ca2d9324c1d4a9d64389beb5"));
executeTest("test reverse trim", spec); executeTest("test reverse trim", spec);
} }
@ -85,7 +85,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test @Test
public void testMismatchedPLs() { public void testMismatchedPLs() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1, "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
Arrays.asList("3c006b06b17bbe8e787d64eff6a63a19")); Arrays.asList("3c006b06b17bbe8e787d64eff6a63a19"));
executeTest("test mismatched PLs", spec); executeTest("test mismatched PLs", spec);
} }
@ -156,7 +156,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test @Test
public void testSLOD() { public void testSLOD() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, "-T UnifiedGenotyper -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("c7429e670ba477bf9a6bbee2fb41c5a9")); Arrays.asList("c7429e670ba477bf9a6bbee2fb41c5a9"));
executeTest("test SLOD", spec); executeTest("test SLOD", spec);
} }
@ -173,7 +173,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testCompTrack() { public void testCompTrack() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("8a9b424e00cdbe6b5e73d517335b2186")); Arrays.asList("a6de72c5197f152be98a6f9029091a9e"));
executeTest("test using comp track", spec); executeTest("test using comp track", spec);
} }