Changes to the Unified Genotyper's arguments:
1. User can specify 4 confidence thresholds: for calling vs. emitting and at standard vs. 'trigger' sites. 2. User can cap the base quality by the read's mapping quality (not done yet). 3. Default confidence threshold is now Q30. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3281 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
8b2ce128b5
commit
850f36aa61
|
|
@ -37,8 +37,16 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
|
|||
// the alternate allele with the largest sum of quality scores
|
||||
protected Character bestAlternateAllele = null;
|
||||
|
||||
// are we at a 'trigger' track site?
|
||||
protected boolean atTriggerTrack = false;
|
||||
|
||||
protected JointEstimateGenotypeCalculationModel() {}
|
||||
// the standard filter to use for calls below the confidence threshold but above the emit threshold
|
||||
protected static final Set<String> filter = new HashSet<String>(1);
|
||||
|
||||
|
||||
protected JointEstimateGenotypeCalculationModel() {
|
||||
filter.add("LowQual");
|
||||
}
|
||||
|
||||
public VariantCallContext callExtendedLocus(RefMetaDataTracker tracker, char[] ref, GenomeLoc loc, Map<String, StratifiedAlignmentContext> stratifiedContexts) {
|
||||
return null;
|
||||
|
|
@ -55,12 +63,12 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
|
|||
initializeBestAlternateAllele(ref, contexts);
|
||||
|
||||
// did we trigger on the provided track?
|
||||
boolean triggerTrack = tracker.getReferenceMetaData(UnifiedGenotyperEngine.TRIGGER_TRACK_NAME, false).size() > 0;
|
||||
atTriggerTrack = tracker.getReferenceMetaData(UnifiedGenotyperEngine.TRIGGER_TRACK_NAME, false).size() > 0;
|
||||
|
||||
// if there are no non-ref bases...
|
||||
if ( bestAlternateAllele == null ) {
|
||||
// if we don't want all bases, then we don't need to calculate genotype likelihoods
|
||||
if ( !triggerTrack && !UAC.ALL_BASES_MODE && !UAC.GENOTYPE_MODE ) {
|
||||
if ( !atTriggerTrack && !UAC.ALL_BASES_MODE && !UAC.GENOTYPE_MODE ) {
|
||||
VariantCallContext vcc = new VariantCallContext(false);
|
||||
estimateReferenceConfidence(vcc, contexts, DiploidGenotypePriors.HUMAN_HETEROZYGOSITY, false);
|
||||
return vcc;
|
||||
|
|
@ -80,7 +88,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
|
|||
if ( verboseWriter != null )
|
||||
printAlleleFrequencyData(ref, loc, frequencyEstimationPoints);
|
||||
|
||||
VariantCallContext vcc = createCalls(tracker, ref, contexts, loc, frequencyEstimationPoints, triggerTrack);
|
||||
VariantCallContext vcc = createCalls(tracker, ref, contexts, loc, frequencyEstimationPoints);
|
||||
|
||||
// technically, at this point our confidence in a reference call isn't accurately
|
||||
// estimated because it didn't take into account samples with no data
|
||||
|
|
@ -190,7 +198,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
|
|||
P_of_ref *= 1.0 - (theta / 2.0) * MathUtils.binomialProbability(0, depth, 0.5);
|
||||
}
|
||||
|
||||
vcc.confidentlyCalled = QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= UAC.CONFIDENCE_THRESHOLD;
|
||||
vcc.confidentlyCalled = QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING;
|
||||
}
|
||||
|
||||
protected void calculateAlleleFrequencyPosteriors(char ref, int frequencyEstimationPoints, Map<String, StratifiedAlignmentContext> contexts, StratifiedAlignmentContext.StratifiedContextType contextType) {
|
||||
|
|
@ -326,7 +334,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
|
|||
return new HashMap<String, Genotype>();
|
||||
}
|
||||
|
||||
protected VariantCallContext createCalls(RefMetaDataTracker tracker, char ref, Map<String, StratifiedAlignmentContext> contexts, GenomeLoc loc, int frequencyEstimationPoints, boolean triggerTrack) {
|
||||
protected VariantCallContext createCalls(RefMetaDataTracker tracker, char ref, Map<String, StratifiedAlignmentContext> contexts, GenomeLoc loc, int frequencyEstimationPoints) {
|
||||
// only need to look at the most likely alternate allele
|
||||
int indexOfMax = BaseUtils.simpleBaseToBaseIndex(bestAlternateAllele);
|
||||
|
||||
|
|
@ -350,8 +358,8 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
|
|||
}
|
||||
|
||||
// return a null call if we don't pass the confidence cutoff or the most likely allele frequency is zero
|
||||
if ( !triggerTrack && !UAC.ALL_BASES_MODE && ((!UAC.GENOTYPE_MODE && bestAFguess == 0) || phredScaledConfidence < UAC.CONFIDENCE_THRESHOLD) )
|
||||
return new VariantCallContext(phredScaledConfidence >= UAC.CONFIDENCE_THRESHOLD);
|
||||
if ( !UAC.ALL_BASES_MODE && !passesEmitThreshold(phredScaledConfidence, bestAFguess) )
|
||||
return new VariantCallContext(passesCallThreshold(phredScaledConfidence));
|
||||
|
||||
// output to beagle file if requested
|
||||
if ( beagleWriter != null ) {
|
||||
|
|
@ -420,8 +428,20 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
|
|||
attributes.put("SB", new Double(strandScore));
|
||||
}
|
||||
|
||||
VariantContext vc = new VariantContext("UG_SNP_call", loc, alleles, genotypes, phredScaledConfidence/10.0, null, attributes);
|
||||
VariantContext vc = new VariantContext("UG_SNP_call", loc, alleles, genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence) ? null : filter, attributes);
|
||||
|
||||
return new VariantCallContext(vc, phredScaledConfidence >= UAC.CONFIDENCE_THRESHOLD);
|
||||
return new VariantCallContext(vc, passesCallThreshold(phredScaledConfidence));
|
||||
}
|
||||
|
||||
protected boolean passesEmitThreshold(double conf, int bestAFguess) {
|
||||
return (atTriggerTrack ?
|
||||
(conf >= Math.min(UAC.TRIGGER_CONFIDENCE_FOR_CALLING, UAC.TRIGGER_CONFIDENCE_FOR_EMITTING)) :
|
||||
((UAC.GENOTYPE_MODE || bestAFguess != 0) && conf >= Math.min(UAC.STANDARD_CONFIDENCE_FOR_CALLING, UAC.STANDARD_CONFIDENCE_FOR_EMITTING)));
|
||||
}
|
||||
|
||||
protected boolean passesCallThreshold(double conf) {
|
||||
return (atTriggerTrack ?
|
||||
(conf >= UAC.TRIGGER_CONFIDENCE_FOR_CALLING) :
|
||||
(conf >= UAC.STANDARD_CONFIDENCE_FOR_CALLING));
|
||||
}
|
||||
}
|
||||
|
|
@ -40,9 +40,6 @@ public class UnifiedArgumentCollection {
|
|||
@Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false)
|
||||
public Double heterozygosity = DiploidGenotypePriors.HUMAN_HETEROZYGOSITY;
|
||||
|
||||
@Argument(fullName = "poolSize", shortName = "ps", doc = "Number of individuals in the pool -- no longer in use", required = false)
|
||||
public int POOLSIZE = 0;
|
||||
|
||||
// control the output
|
||||
@Argument(fullName = "genotype", shortName = "genotype", doc = "Should we output confident genotypes (i.e. including ref calls) or just the variants?", required = false)
|
||||
public boolean GENOTYPE_MODE = false;
|
||||
|
|
@ -50,6 +47,18 @@ public class UnifiedArgumentCollection {
|
|||
@Argument(fullName = "output_all_callable_bases", shortName = "all_bases", doc = "Should we output all callable bases?", required = false)
|
||||
public boolean ALL_BASES_MODE = false;
|
||||
|
||||
@Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called", required = false)
|
||||
public double STANDARD_CONFIDENCE_FOR_CALLING = 30.0;
|
||||
|
||||
@Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)", required = false)
|
||||
public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0;
|
||||
|
||||
@Argument(fullName = "trigger_min_confidence_threshold_for_calling", shortName = "trig_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants at 'trigger' track sites should be called", required = false)
|
||||
public double TRIGGER_CONFIDENCE_FOR_CALLING = 30.0;
|
||||
|
||||
@Argument(fullName = "trigger_min_confidence_threshold_for_emitting", shortName = "trig_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)", required = false)
|
||||
public double TRIGGER_CONFIDENCE_FOR_EMITTING = 30.0;
|
||||
|
||||
@Argument(fullName = "noSLOD", shortName = "nsl", doc = "If provided, we will not calculate the SLOD", required = false)
|
||||
public boolean NO_SLOD = false;
|
||||
|
||||
|
|
@ -63,9 +72,6 @@ public class UnifiedArgumentCollection {
|
|||
|
||||
|
||||
// control the various parameters to be used
|
||||
@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 = 50.0;
|
||||
|
||||
@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 = 10;
|
||||
|
||||
|
|
@ -81,6 +87,9 @@ public class UnifiedArgumentCollection {
|
|||
@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;
|
||||
|
||||
@Argument(fullName = "cap_base_quality_by_mapping_quality", shortName = "cap_base_qual", doc = "Cap the base quality of any given base by its read's mapping quality", required = false)
|
||||
public boolean CAP_BASE_QUALITY = false;
|
||||
|
||||
|
||||
public UnifiedArgumentCollection clone() {
|
||||
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
|
||||
|
|
@ -93,7 +102,10 @@ public class UnifiedArgumentCollection {
|
|||
uac.NO_SLOD = NO_SLOD;
|
||||
uac.ASSUME_SINGLE_SAMPLE = ASSUME_SINGLE_SAMPLE;
|
||||
uac.defaultPlatform = defaultPlatform;
|
||||
uac.CONFIDENCE_THRESHOLD = CONFIDENCE_THRESHOLD;
|
||||
uac.STANDARD_CONFIDENCE_FOR_CALLING = STANDARD_CONFIDENCE_FOR_CALLING;
|
||||
uac.STANDARD_CONFIDENCE_FOR_EMITTING = STANDARD_CONFIDENCE_FOR_EMITTING;
|
||||
uac.TRIGGER_CONFIDENCE_FOR_CALLING = TRIGGER_CONFIDENCE_FOR_CALLING;
|
||||
uac.TRIGGER_CONFIDENCE_FOR_EMITTING = TRIGGER_CONFIDENCE_FOR_EMITTING;
|
||||
uac.MIN_BASE_QUALTY_SCORE = MIN_BASE_QUALTY_SCORE;
|
||||
uac.MIN_MAPPING_QUALTY_SCORE = MIN_MAPPING_QUALTY_SCORE;
|
||||
uac.MAX_MISMATCHES = MAX_MISMATCHES;
|
||||
|
|
|
|||
|
|
@ -105,9 +105,6 @@ public class UnifiedGenotyperEngine {
|
|||
if ( UAC.genotypeModel == GenotypeCalculationModel.Model.INDELS && !(genotypeWriter instanceof VCFGenotypeWriter) ) {
|
||||
throw new IllegalArgumentException("Attempting to use an output format other than VCF with indels. Please set the output format to VCF.");
|
||||
}
|
||||
if ( UAC.POOLSIZE > 0 ) {
|
||||
throw new IllegalArgumentException("Attempting to provide depreciated POOLSIZE parameter for retired POOLED model");
|
||||
}
|
||||
if ( toolkit.getArguments().numberOfThreads > 1 && UAC.ASSUME_SINGLE_SAMPLE != null ) {
|
||||
// the ASSUME_SINGLE_SAMPLE argument can't be handled (at least for now) while we are multi-threaded because the IO system doesn't know how to get the sample name
|
||||
throw new IllegalArgumentException("For technical reasons, the ASSUME_SINGLE_SAMPLE argument cannot be used with multiple threads");
|
||||
|
|
@ -183,7 +180,7 @@ public class UnifiedGenotyperEngine {
|
|||
pileup = filterPileup(pileup, refContext);
|
||||
|
||||
// don't call when there is no coverage
|
||||
if ( pileup.size() == 0 )
|
||||
if ( pileup.size() == 0 && !UAC.ALL_BASES_MODE )
|
||||
return null;
|
||||
|
||||
// stratify the AlignmentContext and cut by sample
|
||||
|
|
@ -204,7 +201,7 @@ public class UnifiedGenotyperEngine {
|
|||
pileup = filterPileup(pileup, refContext);
|
||||
|
||||
// don't call when there is no coverage
|
||||
if ( pileup.size() == 0 )
|
||||
if ( pileup.size() == 0 && !UAC.ALL_BASES_MODE )
|
||||
return null;
|
||||
|
||||
// are there too many deletions in the pileup?
|
||||
|
|
|
|||
|
|
@ -60,7 +60,7 @@ public class SnpCallRateByCoverageWalker extends LocusWalker<List<String>, Strin
|
|||
|
||||
public void initialize() {
|
||||
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
|
||||
uac.CONFIDENCE_THRESHOLD = confidence;
|
||||
uac.STANDARD_CONFIDENCE_FOR_CALLING = uac.STANDARD_CONFIDENCE_FOR_EMITTING = confidence;
|
||||
uac.ALL_BASES_MODE = true;
|
||||
UG = new UnifiedGenotyperEngine(getToolkit(), uac);
|
||||
|
||||
|
|
|
|||
|
|
@ -68,7 +68,7 @@ public class FindContaminatingReadGroupsWalker extends LocusWalker<Integer, Inte
|
|||
|
||||
public void initialize() {
|
||||
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
|
||||
uac.CONFIDENCE_THRESHOLD = 50;
|
||||
uac.STANDARD_CONFIDENCE_FOR_CALLING = uac.STANDARD_CONFIDENCE_FOR_EMITTING = 50.0;
|
||||
ug = new UnifiedGenotyperEngine(getToolkit(), uac);
|
||||
|
||||
altTable = new NamedTable();
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ public class SecondaryBaseTransitionTableWalker extends LocusWalker<Integer, Int
|
|||
|
||||
public void initialize() {
|
||||
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
|
||||
uac.CONFIDENCE_THRESHOLD = 50;
|
||||
uac.STANDARD_CONFIDENCE_FOR_CALLING = uac.STANDARD_CONFIDENCE_FOR_EMITTING = 50.0;
|
||||
uac.ALL_BASES_MODE = true;
|
||||
ug = new UnifiedGenotyperEngine(getToolkit(), uac);
|
||||
|
||||
|
|
|
|||
|
|
@ -34,24 +34,24 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
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("2a31f997f9c07b6259cf3cdf2459c74b"));
|
||||
"-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", 1,
|
||||
Arrays.asList("d50ebc40d935ece7e57aafc7355bec77"));
|
||||
executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
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("2ab8e48cd7a3d0474e187c2af9694628"));
|
||||
"-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", 1,
|
||||
Arrays.asList("2f113c2b1cd0d36522fc24e7784a2b7d"));
|
||||
executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
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("ed35f375beb0ac849bfe98daffc1cee2"));
|
||||
"-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", 1,
|
||||
Arrays.asList("4f08c27ada3ad1a33d12d106bc80dab6"));
|
||||
executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
|
||||
}
|
||||
|
||||
|
|
@ -63,8 +63,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
@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("75488092bb229d6345b84d9b793e4e55"));
|
||||
"-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 -nt 4", 1,
|
||||
Arrays.asList("d643e60343c05817dcb4fafb7870804d"));
|
||||
executeTest("test parallelization", spec);
|
||||
}
|
||||
|
||||
|
|
@ -77,15 +77,15 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testParameter() {
|
||||
HashMap<String, String> e = new HashMap<String, String>();
|
||||
e.put( "-genotype", "02316b8892d439e23d6fbbc65232f921" );
|
||||
e.put( "-all_bases", "bcce54904e4c3352168bbfb39f2b9a2f" );
|
||||
e.put( "--min_base_quality_score 26", "a8a286e61af8a6b9ba72c2eab19573bb" );
|
||||
e.put( "--min_mapping_quality_score 26", "c599b0c3a1e42772e9d1f9ff7112d1e4" );
|
||||
e.put( "--max_mismatches_in_40bp_window 5", "46129c47e7d283d8950e029ed39dc1e8" );
|
||||
e.put( "-genotype", "310d3f8ac2a1100d82fe6241e201e1d8" );
|
||||
e.put( "-all_bases", "470196b3f9a2ed622383e25552972a3e" );
|
||||
e.put( "--min_base_quality_score 26", "a1142c69f1951a05d5a33215c69133af" );
|
||||
e.put( "--min_mapping_quality_score 26", "796d1ea790481a1a257609279f8076bb" );
|
||||
e.put( "--max_mismatches_in_40bp_window 5", "379bd56d4402e974127e0677ff51d040" );
|
||||
|
||||
for ( Map.Entry<String, String> entry : e.entrySet() ) {
|
||||
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 30 " + entry.getKey(), 1,
|
||||
"-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 " + entry.getKey(), 1,
|
||||
Arrays.asList(entry.getValue()));
|
||||
executeTest(String.format("testParameter[%s]", entry.getKey()), spec);
|
||||
}
|
||||
|
|
@ -93,10 +93,15 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
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("64c8fffc735f72663f27b2257fff5583"));
|
||||
executeTest("testConfidence", spec);
|
||||
WalkerTest.WalkerTestSpec spec1 = 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 -stand_call_conf 10 ", 1,
|
||||
Arrays.asList("7b41dc669e8a0abde089d7aeedab2941"));
|
||||
executeTest("testConfidence1", spec1);
|
||||
|
||||
WalkerTest.WalkerTestSpec spec2 = 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 -stand_emit_conf 10 ", 1,
|
||||
Arrays.asList("258617b8de0e6468bf6a0c740b51676b"));
|
||||
executeTest("testConfidence2", spec2);
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------------------------------------------------
|
||||
|
|
@ -106,19 +111,15 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
// --------------------------------------------------------------------------------------------------------------
|
||||
@Test
|
||||
public void testOtherOutput() {
|
||||
String[] md5s = {"e9d7c27ed63d2e92a17ba44501ab1138", "8cba0b8752f18fc620b4697840bc7291"};
|
||||
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" +
|
||||
" -varout /dev/null" +
|
||||
" -beagle %s" +
|
||||
" -L 1:10,023,400-10,024,000" +
|
||||
" -bm empirical" +
|
||||
" -gm JOINT_ESTIMATE" +
|
||||
" -vf VCF",
|
||||
2,
|
||||
Arrays.asList(md5s));
|
||||
" -L 1:10,023,400-10,024,000",
|
||||
1,
|
||||
Arrays.asList("5077d80806e24865b5c12553843a5f85"));
|
||||
|
||||
executeTest(String.format("testOtherOutput"), spec);
|
||||
}
|
||||
|
|
@ -137,7 +138,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
|
||||
for ( Map.Entry<String, String> entry : e.entrySet() ) {
|
||||
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 -vf " + entry.getKey(), 1,
|
||||
"-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 -vf " + entry.getKey(), 1,
|
||||
Arrays.asList(entry.getValue()));
|
||||
executeTest(String.format("testOtherFormat[%s]", entry.getKey()), spec);
|
||||
}
|
||||
|
|
@ -160,7 +161,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
|
||||
for ( Map.Entry<Double, String> entry : e.entrySet() ) {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -vf GELI -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 --heterozygosity " + entry.getKey(), 1,
|
||||
"-T UnifiedGenotyper -vf GELI -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 --heterozygosity " + entry.getKey(), 1,
|
||||
Arrays.asList(entry.getValue()));
|
||||
executeTest(String.format("testHeterozyosity[%s]", entry.getKey()), spec);
|
||||
}
|
||||
|
|
@ -180,7 +181,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
|
||||
for ( Map.Entry<String, String> entry : e.entrySet() ) {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -vf GELI -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 -gm JOINT_ESTIMATE -confidence 30 -bm " + entry.getKey(), 1,
|
||||
"-T UnifiedGenotyper -vf GELI -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 " + entry.getKey(), 1,
|
||||
Arrays.asList(entry.getValue()));
|
||||
executeTest(String.format("testOtherBaseCallModel[%s]", entry.getKey()), spec);
|
||||
}
|
||||
|
|
@ -199,11 +200,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
" -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" +
|
||||
" -varout %s" +
|
||||
" -L 1:10,000,000-10,100,000" +
|
||||
" -bm empirical" +
|
||||
" -gm JOINT_ESTIMATE" +
|
||||
" -vf GELI",
|
||||
" -vf GELI",
|
||||
1,
|
||||
Arrays.asList("3c6d76d55d608482940cd725b87ef07d"));
|
||||
Arrays.asList("f67c690bf2e4eee2bb7c58b6646a2a98"));
|
||||
|
||||
executeTest(String.format("testMultiTechnologies"), spec);
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue