Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.Genotype

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            beagleOut.append(allele.isNoCall() ? "-" : allele.getBaseString()).append(" ");
        }

        // write out sample level genotypes
        for ( String sample : samples ) {
            Genotype genotype = vc.getGenotype(sample);
            if ( ! makeMissing && genotype.isCalled() ) {
                addAlleles(beagleOut, genotype);
            } else {
                addAlleles(beagleOut, MISSING, MISSING);
            }
        }
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        TruthState truthState = null;
        CallState callState = null;

        // TODO: what about getPloidy()

        Genotype truthGenotype = null, callGenotype = null;

        // Site level checks
        if (truthContext == null) truthState = TruthState.MISSING;
        else if (truthContext.isMixed()) truthState = TruthState.IS_MIXED;
        else if (truthContext.isFiltered()) truthState = TruthState.VC_FILTERED;
        else {
            // Genotype level checks
            truthGenotype = truthContext.getGenotype(truthSample);
            if (truthGenotype.isNoCall())           truthState = TruthState.NO_CALL;
            else if (truthGenotype.isFiltered())    truthState = TruthState.GT_FILTERED;
            else if ((truthGenotype.getGQ() != -1) && (truthGenotype.getGQ() < minGq)) truthState = TruthState.LOW_GQ;
            else if ((truthGenotype.getDP() != -1) && (truthGenotype.getDP() < minDp)) truthState = TruthState.LOW_DP;
            // Note.  Genotype.isMixed means that it is called on one chromosome and NOT on the other
            else if ((truthGenotype.isMixed())) truthState = TruthState.NO_CALL;
        }

        // Site level checks
        if (callContext == null) callState = CallState.MISSING;
        else if (callContext.isMixed()) callState = CallState.IS_MIXED;
        else if (callContext.isFiltered()) callState = CallState.VC_FILTERED;
        else {
            // Genotype level checks
            callGenotype = callContext.getGenotype(callSample);
            if (callGenotype.isNoCall())           callState = CallState.NO_CALL;
            else if (callGenotype.isFiltered())    callState = CallState.GT_FILTERED;
            else if ((callGenotype.getGQ() != -1) && (callGenotype.getGQ() < minGq)) callState = CallState.LOW_GQ;
            else if ((callGenotype.getDP() != -1) && (callGenotype.getDP() < minDp)) callState = CallState.LOW_DP;
                // Note.  Genotype.isMixed means that it is called on one chromosome and NOT on the other
            else if ((callGenotype.isMixed())) callState = CallState.NO_CALL;
        }

        // initialize the reference
        String truthRef = (truthContext != null) ? truthContext.getReference().getBaseString() : null;
        String callRef  = (callContext != null) ?  callContext.getReference().getBaseString() : null;

        String truthAllele1 = null;
        String truthAllele2 = null;
        if (null == truthState) {
            // Truth State not yet determined - will need to use truth genotypes below
            if (truthGenotype.getAlleles().size() != 2) {
                throw new IllegalStateException("Genotype for Variant Context: " + truthContext + " does not have exactly 2 alleles");
            }
            truthAllele1 = truthGenotype.getAllele(0).getBaseString();
            truthAllele2 = truthGenotype.getAllele(1).getBaseString();
        }

        String callAllele1 = null;
        String callAllele2 = null;
        if (null == callState) {
            if (callGenotype.getAlleles().size() != 2) {
                throw new IllegalStateException("Genotype for Variant Context: " + callContext + " does not have exactly 2 alleles");
            }
            callAllele1 = callGenotype.getAllele(0).getBaseString();
            callAllele2 = callGenotype.getAllele(1).getBaseString();
        }

        if ((truthRef != null && callRef != null) && (!truthRef.equals(callRef))) {
            // This is for dealing with indel conditions, where we can have truth being TCAA*/T, call being TCAACAA*/TCAA (*=ref)
            // So, we want to verify that both refs start with the shorter substring of the two
            // and then we want to pad the shorter's ref and alleles, so that TCAA*/T becomes TCAACAA*/TCAA (i.e. tacking on the CAA)
            if (truthRef.length() < callRef.length()) {
                // Truth reference is shorter than call reference
                final String suffix = getStringSuffix(callRef, truthRef, "Ref alleles mismatch between: " + truthContext + " and " + callContext);
                truthRef = truthRef + suffix;
                if (null == truthState) {
                    truthAllele1 = truthGenotype.getAllele(0).getBaseString() + suffix;
                    truthAllele2 = truthGenotype.getAllele(1).getBaseString() + suffix;
                }
            }
            else if (truthRef.length() > callRef.length()) {
                // call reference is shorter than truth:
                final String suffix = getStringSuffix(truthRef, callRef, "Ref alleles mismatch between: " + truthContext + " and " + callContext);
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    @Test(dataProvider = "genotypeConcordanceDetermineStateDataProvider")
    public void testGenotypeConcordanceDetermineState(final Allele truthAllele1, final Allele truthAllele2, final TruthState expectedTruthState,
                                                      final Allele callAllele1, final Allele callAllele2, final CallState expectedCallState) throws Exception {
        final List<Allele> truthAlleles = makeUniqueListOfAlleles(truthAllele1, truthAllele2);
        final Genotype truthGt = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(truthAllele1, truthAllele2));

        final VariantContext truthVariantContext = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, truthAlleles).genotypes(truthGt).make();

        final List<Allele> callAlleles = makeUniqueListOfAlleles(callAllele1, callAllele2);
        final Genotype callGt = GenotypeBuilder.create(CALL_SAMPLE_NAME, Arrays.asList(callAllele1, callAllele2));
        final VariantContext callVariantContext = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, callAlleles).genotypes(callGt).make();

        testGenotypeConcordanceDetermineState(truthVariantContext, expectedTruthState, callVariantContext, expectedCallState, 0, 0);
    }
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    }

    @Test
    public void testGenotypeConcordanceDetermineStateNull() throws Exception {
        final List<Allele> alleles = makeUniqueListOfAlleles(Aref, C);
        final Genotype gt1 = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C));
        final VariantContext vc1 = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles).genotypes(gt1).make();

        testGenotypeConcordanceDetermineState(null, TruthState.MISSING, null, CallState.MISSING, 0, 0);
        testGenotypeConcordanceDetermineState(vc1, TruthState.HET_REF_VAR1, null, CallState.MISSING, 0, 0);
        testGenotypeConcordanceDetermineState(null, TruthState.MISSING, vc1, CallState.HET_REF_VAR1, 0, 0);
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    public void testGenotypeConcordanceDetermineStateFilter() throws Exception {
        final Set<String> filters = new HashSet<String>(Arrays.asList("BAD!"));

        // Filtering on the variant context
        final List<Allele> alleles1 = makeUniqueListOfAlleles(Aref, C);
        final Genotype gt1 = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C));
        final VariantContext vcFiltered = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles1).genotypes(gt1).filters(filters).make();

        final List<Allele> alleles2 = makeUniqueListOfAlleles(Aref, T);
        final Genotype gt2 = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, T));
        final VariantContext vcNotFiltered = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles2).genotypes(gt2).make();

        testGenotypeConcordanceDetermineState(vcFiltered, TruthState.VC_FILTERED, vcNotFiltered, CallState.HET_REF_VAR1, 0, 0);
        testGenotypeConcordanceDetermineState(vcNotFiltered, TruthState.HET_REF_VAR1, vcFiltered, CallState.VC_FILTERED, 0, 0);
        testGenotypeConcordanceDetermineState(vcFiltered, TruthState.VC_FILTERED, vcFiltered, CallState.VC_FILTERED, 0, 0);

        // Filtering on the genotype
        final List<String> gtFilters = new ArrayList<String>(Arrays.asList("WICKED"));
        final List<Allele> alleles3 = makeUniqueListOfAlleles(Aref, C);
        final Genotype gt3 = new GenotypeBuilder(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C)).filters(gtFilters).make();
        final VariantContext vcGtFiltered = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles3).genotypes(gt3).make();

        testGenotypeConcordanceDetermineState(vcGtFiltered, TruthState.GT_FILTERED, vcNotFiltered, CallState.HET_REF_VAR1, 0, 0);
        testGenotypeConcordanceDetermineState(vcNotFiltered, TruthState.HET_REF_VAR1, vcGtFiltered, CallState.GT_FILTERED, 0, 0);
        testGenotypeConcordanceDetermineState(vcGtFiltered, TruthState.GT_FILTERED, vcGtFiltered, CallState.GT_FILTERED, 0, 0);
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    }

    @Test
    public void testGenotypeConcordanceDetermineStateDp() throws Exception {
        final List<Allele> allelesNormal = makeUniqueListOfAlleles(Aref, C);
        final Genotype gtNormal = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C));
        final VariantContext vcNormal = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, allelesNormal).genotypes(gtNormal).make();

        final List<Allele> allelesLowDp = makeUniqueListOfAlleles(Aref, C);
        final Genotype gtLowDp = new GenotypeBuilder(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C)).DP(4).make();
        final VariantContext vcLowDp = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, allelesLowDp).genotypes(gtLowDp).make();

        testGenotypeConcordanceDetermineState(vcLowDp, TruthState.LOW_DP, vcNormal, CallState.HET_REF_VAR1, 0, 20);
        testGenotypeConcordanceDetermineState(vcLowDp, TruthState.HET_REF_VAR1, vcLowDp, CallState.HET_REF_VAR1, 0, 2);
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    }

    @Test
    public void testGenotypeConcordanceDetermineStateGq() throws Exception {
        final List<Allele> allelesNormal = makeUniqueListOfAlleles(Aref, C);
        final Genotype gtNormal = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C));
        final VariantContext vcNormal = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, allelesNormal).genotypes(gtNormal).make();

        final List<Allele> allelesLowGq = makeUniqueListOfAlleles(Aref, C);
        final Genotype gtLowGq = new GenotypeBuilder(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C)).GQ(4).make();
        final VariantContext vcLowGq = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, allelesLowGq).genotypes(gtLowGq).make();

        testGenotypeConcordanceDetermineState(vcLowGq, TruthState.LOW_GQ, vcNormal, CallState.HET_REF_VAR1, 20, 0);
        testGenotypeConcordanceDetermineState(vcLowGq, TruthState.HET_REF_VAR1, vcLowGq, CallState.HET_REF_VAR1, 2, 0);
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Related Classes of htsjdk.variant.variantcontext.Genotype

  • org.broad.igv.plugin.mongovariant.VariantReviewDialog
  • org.broad.igv.plugin.mongovariant.VariantReviewSource
  • org.broadinstitute.gatk.tools.walkers.beagle.VariantsToBeagleUnphased
  • org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculatorProvider
  • org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.IndependentAllelesDiploidExactAFCalculatorUnitTest
  • org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyperIntegrationTest
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.ReferenceConfidenceModelUnitTest
  • org.broadinstitute.gatk.utils.gvcf.GVCFWriter
  • org.broadinstitute.gatk.utils.MendelianViolation
  • picard.vcf.GenotypeConcordance
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