htsjdk.variant.variantcontext.Genotype#isHomVar

Source File: VariantContextSingletonFilter.java From Drop-seq with MIT License

6 votes

@Override
/**
 * For each variant context, look at the genotypes of the samples, and count the number of samples that have
 * an alternate allele.  If that number of samples!=1, return true to filter this record.
 * @param rec
 * @return
 */
public boolean filterOut(final VariantContext rec) {
	GenotypesContext gc = rec.getGenotypes();
	Iterator<Genotype> iter = gc.iterator();
	int count=0;
	while (iter.hasNext()) {
		Genotype g = iter.next();
		// boolean isHet = g.isHet();
		// boolean homRef = g.isHomRef();

		if (hetVarOnly & g.isHomVar())
			return true; // filter when het only and observe hom_var.
		if (g.isHet() || g.isHomVar())
			count++;
	}
	if (count==1) return false;
	return true;
}

Source File: CallingMetricAccumulator.java From picard with MIT License

6 votes

private void updateDetailMetric(final VariantCallingDetailMetrics metric,
                                final Genotype genotype,
                                final VariantContext vc,
                                final boolean hasSingletonSample) {
    updateSummaryMetric(metric, genotype, vc, hasSingletonSample);

    if (genotype != null && !vc.isFiltered()) {
        if (genotype.getGQ() == 0) {
            ++metric.TOTAL_GQ0_VARIANTS;
        }
        if (genotype.isHet()) {
            ++metric.numHets;
        } else if (genotype.isHomVar()) {
            ++metric.numHomVar;
        }
    }
}

Source File: MendelianViolation.java From gatk with BSD 3-Clause "New" or "Revised" License

6 votes

/**
 * Evaluate the genotypes of mom, dad, and child to detect Mendelian violations
 *
 * @param gMom
 * @param gDad
 * @param gChild
 * @return true if the three genotypes represent a Mendelian violation; false otherwise
 */
public static boolean isViolation(final Genotype gMom, final Genotype gDad, final Genotype gChild) {
    if (gChild.isNoCall()){ //cannot possibly be a violation is child is no call
        return false;
    }
    if(gMom.isHomRef() && gDad.isHomRef() && gChild.isHomRef()) {
        return false;
    }

    //1 parent is no "call
    if(!gMom.isCalled()){
        return (gDad.isHomRef() && gChild.isHomVar()) || (gDad.isHomVar() && gChild.isHomRef());
    }
    else if(!gDad.isCalled()){
        return (gMom.isHomRef() && gChild.isHomVar()) || (gMom.isHomVar() && gChild.isHomRef());
    }
    //Both parents have genotype information
    final Allele childRef = gChild.getAlleles().get(0);
    return !(gMom.getAlleles().contains(childRef) && gDad.getAlleles().contains(gChild.getAlleles().get(1)) ||
        gMom.getAlleles().contains(gChild.getAlleles().get(1)) && gDad.getAlleles().contains(childRef));
}

Source File: FastaAlternateReferenceMaker.java From gatk with BSD 3-Clause "New" or "Revised" License

6 votes

/**
 * Returns the IUPAC encoding for the given genotype or the reference base if not possible
 *
 * @param genotype  the genotype to encode
 * @return non-null, non-empty String of bases
 */
private String getIUPACBase(final Genotype genotype) {
    Utils.nonNull(genotype, () -> "The genotype is null for sample " + iupacSample);

    // If we have a spanning deletion, if both alleles are spanning deletions, use the empty allele. Otherwise, use the allele that is not a
    // spanning deletion.
    if ( genotype.getAlleles().contains(Allele.SPAN_DEL) ) {
        if ( genotype.isHomVar() ) {
            return EMPTY_BASE;
        } else {
            return genotype.getAllele(0).equals(Allele.SPAN_DEL) ? genotype.getAllele(1).getBaseString() : genotype.getAllele(0).getBaseString();
        }
    }

    if ( !genotype.isHet() ) {
        return genotype.getAllele(0).getBaseString();
    }

    final byte allele1 = genotype.getAllele(0).getBases()[0];
    final byte allele2 = genotype.getAllele(1).getBases()[0];
    return new String(new byte[] {BaseUtils.basesToIUPAC(allele1, allele2)});
}

Source File: AnnotateVcfWithExpectedAlleleFraction.java From gatk-protected with BSD 3-Clause "New" or "Revised" License

5 votes

private static double weight(final Genotype genotype) {
    if (genotype.isHomVar()) {
        return 1.0;
    } else if (genotype.isHet()) {
        return 0.5;
    } else {
        return 0.0;
    }
}

Source File: AnnotateVcfWithExpectedAlleleFraction.java From gatk with BSD 3-Clause "New" or "Revised" License

5 votes

private static double weight(final Genotype genotype) {
    if (genotype.isHomVar()) {
        return 1.0;
    } else if (genotype.isHet()) {
        return 0.5;
    } else {
        return 0.0;
    }
}

Source File: QualByDepth.java From gatk with BSD 3-Clause "New" or "Revised" License

5 votes

public static int getDepth(final GenotypesContext genotypes, final AlleleLikelihoods<GATKRead, Allele> likelihoods) {
    int depth = 0;
    int ADrestrictedDepth = 0;

    for ( final Genotype genotype : genotypes ) {
        // we care only about variant calls with likelihoods
        if ( !genotype.isHet() && !genotype.isHomVar() ) {
            continue;
        }

        // if we have the AD values for this sample, let's make sure that the variant depth is greater than 1!
        if ( genotype.hasAD() ) {
            final int[] AD = genotype.getAD();
            final int totalADdepth = (int) MathUtils.sum(AD);
            if ( totalADdepth != 0 ) {
                if (totalADdepth - AD[0] > 1) {
                    ADrestrictedDepth += totalADdepth;
                }
                depth += totalADdepth;
                continue;
            }
        }
        // if there is no AD value or it is a dummy value, we want to look to other means to get the depth
        if (likelihoods != null) {
            depth += likelihoods.sampleEvidenceCount(likelihoods.indexOfSample(genotype.getSampleName()));
        } else if ( genotype.hasDP() ) {
            depth += genotype.getDP();
        }
    }

    // if the AD-restricted depth is a usable value (i.e. not zero), then we should use that one going forward
    if ( ADrestrictedDepth > 0 ) {
        depth = ADrestrictedDepth;
    }
    return depth;
}

Source File: ArraysCallingMetricAccumulator.java From picard with MIT License

4 votes

private void updateDetailMetric(final CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics metric,
                                final Genotype genotype,
                                final VariantContext vc,
                                final boolean hasSingletonSample) {
    metric.NUM_ASSAYS++;
    if (!vc.isFiltered() || vc.getCommonInfo().getFilters().contains(InfiniumVcfFields.DUPE)) {
        metric.NUM_NON_FILTERED_ASSAYS++;
        if (genotype.isCalled()) {
            metric.NUM_CALLS++;
            String gtA = (String) genotype.getExtendedAttribute(InfiniumVcfFields.GTA, genotype.getGenotypeString());
            if (!gtA.equals(VCFConstants.EMPTY_GENOTYPE)) {
                metric.NUM_AUTOCALL_CALLS++;
            }
        } else {
            metric.NUM_NO_CALLS++;
        }

        if (vc.isSNP()) {
            // Biallelic SNPs
            final boolean isInDbSnp = dbsnp.snps.isDbSnpSite(vc.getContig(), vc.getStart());

            metric.NUM_SNPS++;

            if (isInDbSnp) {
                metric.NUM_IN_DB_SNP++;
            }
        } else if (vc.isIndel()) {
            metric.NUM_INDELS++;
        }

        if (hasSingletonSample) {
            metric.NUM_SINGLETONS++;
        }

        if (genotype.isHet()) {
            metric.numHets++;
        } else if (genotype.isHomVar()) {
            metric.numHomVar++;
        }
    } else {
        metric.NUM_FILTERED_ASSAYS++;
        if (vc.getCommonInfo().getFilters().contains(InfiniumVcfFields.ZEROED_OUT_ASSAY)) {
            // A "zeroed-out SNP".  Marked as unusable/uncallable
            metric.NUM_ZEROED_OUT_ASSAYS++;
        }
    }
}

Java Code Examples for htsjdk.variant.variantcontext.Genotype#isHomVar()