VCF->beagle and VCF phasing using beagle input. Appears to work fairly well. VariantContexts now support phased genotypes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2812 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo
parent
457568485a
commit
94f892ad42
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@ -13,22 +13,23 @@ public class Genotype {
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protected InferredGeneticContext commonInfo;
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public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR;
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protected List<Allele> alleles = new ArrayList<Allele>();
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private boolean genotypesArePhased = false;
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public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
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public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean genotypesArePhased) {
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this.alleles = Collections.unmodifiableList(alleles);
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commonInfo = new InferredGeneticContext(sampleName, negLog10PError, filters, attributes);
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this.genotypesArePhased = genotypesArePhased;
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validate();
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}
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public Genotype(String sampleName, List<Allele> alleles, double negLog10PError) {
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this(sampleName, alleles, negLog10PError, null, null);
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this(sampleName, alleles, negLog10PError, null, null, false);
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}
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public Genotype(String sampleName, List<Allele> alleles) {
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this(sampleName, alleles, NO_NEG_LOG_10PERROR, null, null);
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this(sampleName, alleles, NO_NEG_LOG_10PERROR, null, null, false);
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}
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/**
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* @return the alleles for this genotype
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*/
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@ -63,6 +64,7 @@ public class Genotype {
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return al;
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}
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public boolean genotypesArePhased() { return genotypesArePhased; }
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/**
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* @return the ploidy of this genotype
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@ -123,12 +125,19 @@ public class Genotype {
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throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this);
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}
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private String haplotypesString() {
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if ( genotypesArePhased() )
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return Utils.join("|", getAlleles());
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else
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return Utils.join("/", Utils.sorted(getAlleles()));
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}
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public String toString() {
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return String.format("[GT: %s %s %s Q%.2f %s]", getSampleName(), getAlleles(), getType(), 10 * getNegLog10PError(), Utils.sortedString(getAttributes()));
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return String.format("[GT: %s %s %s Q%.2f %s]", getSampleName(), haplotypesString(), getType(), getPhredScaledQual(), Utils.sortedString(getAttributes()));
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}
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public String toBriefString() {
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return String.format("%s:Q%.2f", getAlleles(), 10 * getNegLog10PError());
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return String.format("%s:Q%.2f", haplotypesString(), getPhredScaledQual());
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}
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public boolean sameGenotype(Genotype other) {
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@ -148,7 +157,7 @@ public class Genotype {
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return false;
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}
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} else {
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List<Allele> otherAlleles = other.getAlleles();
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List<Allele> otherAlleles = new ArrayList<Allele>(other.getAlleles());
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for ( Allele myAllele : getAlleles() ) {
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Allele alleleToRemove = null;
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for ( Allele otherAllele : otherAlleles ) {
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@ -179,6 +188,7 @@ public class Genotype {
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public boolean isNotFiltered() { return commonInfo.isNotFiltered(); }
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public boolean hasNegLog10PError() { return commonInfo.hasNegLog10PError(); }
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public double getNegLog10PError() { return commonInfo.getNegLog10PError(); }
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public double getPhredScaledQual() { return commonInfo.getPhredScaledQual(); }
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public Map<String, Object> getAttributes() { return commonInfo.getAttributes(); }
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public boolean hasAttribute(String key) { return commonInfo.hasAttribute(key); }
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@ -107,6 +107,7 @@ final class InferredGeneticContext {
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* @return the -1 * log10-based error estimate
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*/
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public double getNegLog10PError() { return negLog10PError; }
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public double getPhredScaledQual() { return getNegLog10PError() * 10; }
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public void setNegLog10PError(double negLog10PError) {
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if ( negLog10PError < 0 && negLog10PError != NO_NEG_LOG_10PERROR ) throw new IllegalArgumentException("BUG: negLog10PError cannot be < than 0 : " + negLog10PError);
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@ -9,7 +9,7 @@ import java.util.*;
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*/
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public class MutableGenotype extends Genotype {
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public MutableGenotype(Genotype parent) {
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super(parent.getSampleName(), parent.getAlleles(), parent.getNegLog10PError(), parent.getFilters(), parent.getAttributes());
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super(parent.getSampleName(), parent.getAlleles(), parent.getNegLog10PError(), parent.getFilters(), parent.getAttributes(), parent.genotypesArePhased());
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}
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// todo -- add rest of genotype constructors here
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@ -18,7 +18,7 @@ public class MutableGenotype extends Genotype {
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}
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public Genotype unmodifiableGenotype() {
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return new Genotype(getSampleName(), getAlleles(), getNegLog10PError(), getFilters(), getAttributes());
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return new Genotype(getSampleName(), getAlleles(), getNegLog10PError(), getFilters(), getAttributes(), genotypesArePhased());
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}
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@ -457,6 +457,7 @@ public class VariantContext {
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public boolean isNotFiltered() { return commonInfo.isNotFiltered(); }
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public boolean hasNegLog10PError() { return commonInfo.hasNegLog10PError(); }
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public double getNegLog10PError() { return commonInfo.getNegLog10PError(); }
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public double getPhredScaledQual() { return commonInfo.getPhredScaledQual(); }
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public Map<String, Object> getAttributes() { return commonInfo.getAttributes(); }
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public boolean hasAttribute(String key) { return commonInfo.hasAttribute(key); }
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@ -601,6 +602,8 @@ public class VariantContext {
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*/
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public Map<String, Genotype> getGenotypes() { return genotypes; }
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public List<Genotype> getGenotypesSortedByName() { return Utils.sorted(genotypes); }
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/**
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* Returns a map from sampleName -> Genotype for the genotype associated with sampleName. Returns a map
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* for consistency with the multi-get function.
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@ -652,6 +655,10 @@ public class VariantContext {
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return getGenotypes().containsKey(sample);
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}
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public Genotype getGenotype(int ith) {
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return getGenotypesSortedByName().get(ith);
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}
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/**
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* Returns the number of chromosomes carrying any allele in the genotypes (i.e., excluding NO_CALLS
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@ -833,7 +840,7 @@ public class VariantContext {
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public String toString() {
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return String.format("[VC %s @ %s of type=%s alleles=%s attr=%s GT=%s",
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getName(), getLocation(), this.getType(),
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Utils.sorted(this.getAlleles()), Utils.sortedString(this.getAttributes()), Utils.sorted(this.getGenotypes()));
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Utils.sorted(this.getAlleles()), Utils.sortedString(this.getAttributes()), this.getGenotypesSortedByName());
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}
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// protected basic manipulation routines
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@ -79,7 +79,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
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addModule("VCF", RodVCF.class);
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addModule("PicardDbSNP", rodPicardDbSNP.class);
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addModule("HapmapVCF", HapmapVCFROD.class);
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addModule("Beagle", BeagleROD.class);
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}
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@ -4,6 +4,7 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeEncoding;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
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@ -104,7 +105,7 @@ public class VariantContextAdaptors {
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// --------------------------------------------------------------------------------------------------------------
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//
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// VCF to VariantContext
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// VCF to VariantContext and back again
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//
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// --------------------------------------------------------------------------------------------------------------
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@ -170,7 +171,7 @@ public class VariantContextAdaptors {
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if ( vcfG.isFiltered() ) // setup the FL genotype filter fields
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genotypeFilters.addAll(Arrays.asList(vcfG.getFields().get(VCFGenotypeRecord.GENOTYPE_FILTER_KEY).split(";")));
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Genotype g = new Genotype(vcfG.getSampleName(), genotypeAlleles, pError, genotypeFilters, fields);
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Genotype g = new Genotype(vcfG.getSampleName(), genotypeAlleles, pError, genotypeFilters, fields, vcfG.getPhaseType() == VCFGenotypeRecord.PHASE.PHASED);
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genotypes.put(g.getSampleName(), g);
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}
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@ -180,4 +181,79 @@ public class VariantContextAdaptors {
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} else
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return null; // can't handle anything else
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}
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public static VCFRecord toVCF(VariantContext vc) {
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// deal with the reference
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char referenceBase = 'N'; // by default we'll use N
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if ( vc.getReference().length() == 1 ) {
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referenceBase = (char)vc.getReference().getBases()[0];
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}
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String contig = vc.getLocation().getContig();
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long position = vc.getLocation().getStart();
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String ID = vc.hasAttribute("ID") ? vc.getAttributeAsString("ID") : ".";
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double qual = vc.getPhredScaledQual();
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String filters = vc.isFiltered() ? Utils.join(";", Utils.sorted(vc.getFilters())) : VCFRecord.PASSES_FILTERS;
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Map<Allele, VCFGenotypeEncoding> alleleMap = new HashMap<Allele, VCFGenotypeEncoding>();
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alleleMap.put(Allele.NO_CALL, new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_ALLELE)); // convenience for lookup
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List<VCFGenotypeEncoding> vcfAltAlleles = new ArrayList<VCFGenotypeEncoding>();
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for ( Allele a : vc.getAlleles() ) {
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VCFGenotypeEncoding encoding = new VCFGenotypeEncoding(new String(a.getBases()));
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if ( a.isNonReference() ) {
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vcfAltAlleles.add(encoding);
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}
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alleleMap.put(a, encoding);
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}
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List<String> vcfGenotypeAttributeKeys = new ArrayList<String>(Arrays.asList(VCFGenotypeRecord.GENOTYPE_KEY));
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List<String> vcGenotypeKeys = calcVCFGenotypeKeys(vc);
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if ( vc.hasGenotypes() ) vcfGenotypeAttributeKeys.addAll(vcGenotypeKeys);
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String genotypeFormatString = Utils.join(VCFRecord.GENOTYPE_FIELD_SEPERATOR, vcfGenotypeAttributeKeys);
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List<VCFGenotypeRecord> genotypeObjects = new ArrayList<VCFGenotypeRecord>(vc.getGenotypes().size());
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for ( Genotype g : vc.getGenotypesSortedByName() ) {
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List<VCFGenotypeEncoding> encodings = new ArrayList<VCFGenotypeEncoding>(g.getPloidy());
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for ( Allele a : g.getAlleles() ) {
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encodings.add(alleleMap.get(a));
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}
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VCFGenotypeRecord.PHASE phasing = g.genotypesArePhased() ? VCFGenotypeRecord.PHASE.PHASED : VCFGenotypeRecord.PHASE.UNPHASED;
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VCFGenotypeRecord vcfG = new VCFGenotypeRecord(g.getSampleName(), encodings, phasing);
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if ( ! g.isNoCall() ) {
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for ( String key : vcGenotypeKeys ) {
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String val = key.equals(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY) ? String.format("%.2f", g.getPhredScaledQual()) : g.getAttribute(key).toString();
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vcfG.setField(key, val);
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}
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}
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genotypeObjects.add(vcfG);
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}
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// info fields
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Map<String, String> infoFields = new HashMap<String, String>();
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for ( Map.Entry<String, Object> elt : vc.getAttributes().entrySet() ) {
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String key = elt.getKey();
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String val = elt.getValue().toString();
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if ( ! key.equals("ID") ) {
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infoFields.put(key, val);
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}
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}
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return new VCFRecord(referenceBase, contig, position, ID, vcfAltAlleles, qual, filters, infoFields, genotypeFormatString, genotypeObjects);
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}
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private static List<String> calcVCFGenotypeKeys(VariantContext vc) {
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Set<String> keys = new HashSet<String>();
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for ( Genotype g : vc.getGenotypes().values() ) {
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for ( String key : g.getAttributes().keySet() ) {
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keys.add(key);
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}
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}
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keys.add(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY);
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return Utils.sorted(new ArrayList<String>(keys));
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}
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}
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@ -41,26 +41,36 @@ import java.util.regex.Matcher;
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*/
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public class MendelianViolationEvaluator extends VariantEvaluator {
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long nVariants, nViolations, nOverCalls, nUnderCalls;
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String mom, dad, child;
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TrioStructure trio;
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VariantEval2Walker parent;
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private static Pattern FAMILY_PATTERN = Pattern.compile("(.*)\\+(.*)=(.*)");
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public static class TrioStructure {
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public String mom, dad, child;
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}
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public static TrioStructure parseTrioDescription(String family) {
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Matcher m = FAMILY_PATTERN.matcher(family);
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if ( m.matches() ) {
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TrioStructure trio = new TrioStructure();
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//System.out.printf("Found a family pattern: %s%n", parent.FAMILY_STRUCTURE);
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trio.mom = m.group(1);
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trio.dad = m.group(2);
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trio.child = m.group(3);
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return trio;
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} else {
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throw new IllegalArgumentException("Malformatted family structure string: " + family + " required format is mom+dad=child");
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}
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}
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public MendelianViolationEvaluator(VariantEval2Walker parent) {
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this.parent = parent;
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if ( enabled() ) {
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Matcher m = FAMILY_PATTERN.matcher(parent.FAMILY_STRUCTURE);
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if ( m.matches() ) {
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//System.out.printf("Found a family pattern: %s%n", parent.FAMILY_STRUCTURE);
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mom = m.group(1);
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dad = m.group(2);
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child = m.group(3);
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parent.getLogger().debug(String.format("Found a family pattern: %s mom=%s dad=%s child=%s", parent.FAMILY_STRUCTURE, mom, dad, child));
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} else {
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throw new IllegalArgumentException("Malformatted family structure string: " + parent.FAMILY_STRUCTURE + " required format is mom+dad=child");
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}
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trio = parseTrioDescription(parent.FAMILY_STRUCTURE);
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parent.getLogger().debug(String.format("Found a family pattern: %s mom=%s dad=%s child=%s",
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parent.FAMILY_STRUCTURE, trio.mom, trio.dad, trio.child));
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}
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}
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@ -84,9 +94,9 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
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if ( vc.isBiallelic() && vc.hasGenotypes() ) { // todo -- currently limited to biallelic loci
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nVariants++;
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Genotype momG = vc.getGenotype(mom);
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Genotype dadG = vc.getGenotype(dad);
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Genotype childG = vc.getGenotype(child);
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Genotype momG = vc.getGenotype(trio.mom);
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Genotype dadG = vc.getGenotype(trio.dad);
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Genotype childG = vc.getGenotype(trio.child);
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if ( momG.getNegLog10PError() > getQThreshold() && dadG.getNegLog10PError() > getQThreshold() && childG.getNegLog10PError() > getQThreshold() ) {
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// all genotypes are good, so let's see if child is a violation
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@ -146,15 +156,17 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
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UNDER_CALL, OVER_CALL
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}
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public boolean isViolation(VariantContext vc, Genotype momG, Genotype dadG, Genotype childG ) {
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VariantContext momVC = vc.subContextFromGenotypes(momG);
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VariantContext dadVC = vc.subContextFromGenotypes(dadG);
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public static boolean isViolation(VariantContext vc, Genotype momG, Genotype dadG, Genotype childG ) {
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//VariantContext momVC = vc.subContextFromGenotypes(momG);
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//VariantContext dadVC = vc.subContextFromGenotypes(dadG);
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int i = 0;
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for ( Allele momAllele : momVC.getAlleles() ) {
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for ( Allele dadAllele : dadVC.getAlleles() ) {
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Genotype possibleChild = new Genotype("possibleGenotype" + i, Arrays.asList(momAllele, dadAllele));
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if ( childG.sameGenotype(possibleChild, false) ) {
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return false;
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for ( Allele momAllele : momG.getAlleles() ) {
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for ( Allele dadAllele : dadG.getAlleles() ) {
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if ( momAllele.isCalled() && dadAllele.isCalled() ) {
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Genotype possibleChild = new Genotype("possibleGenotype" + i, Arrays.asList(momAllele, dadAllele));
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if ( childG.sameGenotype(possibleChild, false) ) {
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return false;
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}
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}
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}
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}
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@ -112,7 +112,7 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
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*/
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public VCFRecord(char referenceBase,
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String contig,
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int position,
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long position,
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String ID,
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List<VCFGenotypeEncoding> altBases,
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double qual,
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@ -139,7 +139,7 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
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*/
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private void extractFields(Map<VCFHeader.HEADER_FIELDS, String> columnValues) {
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String chrom = null;
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int position = -1;
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long position = -1;
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for (VCFHeader.HEADER_FIELDS val : columnValues.keySet()) {
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switch (val) {
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@ -467,7 +467,7 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
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mReferenceBase = referenceBase;
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}
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public void setLocation(String chrom, int position) {
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public void setLocation(String chrom, long position) {
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if ( chrom == null )
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throw new IllegalArgumentException("Chromosomes cannot be missing");
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if ( position < 0 )
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@ -598,12 +598,12 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
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builder.append(createInfoString());
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if ( mGenotypeFormatString != null && mGenotypeFormatString.length() > 0 ) {
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try {
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addGenotypeData(builder, header);
|
||||
} catch (Exception e) {
|
||||
if ( validationStringency == VCFGenotypeWriter.VALIDATION_STRINGENCY.STRICT )
|
||||
throw new RuntimeException(e.getMessage());
|
||||
}
|
||||
// try {
|
||||
addGenotypeData(builder, header);
|
||||
// } catch (Exception e) {
|
||||
// if ( validationStringency == VCFGenotypeWriter.VALIDATION_STRINGENCY.STRICT )
|
||||
// throw new RuntimeException(e);
|
||||
// }
|
||||
}
|
||||
|
||||
return builder.toString();
|
||||
|
|
|
|||
|
|
@ -17,11 +17,11 @@ public class VariantContextIntegrationTest extends WalkerTest {
|
|||
|
||||
static HashMap<String, String> expectations = new HashMap<String, String>();
|
||||
static {
|
||||
expectations.put("-L 1:1-10000 --printPerLocus", "39c035ae756eb176a7baffcd0f0fe0af");
|
||||
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "33ab797ac3de900e75fc0d9b01efe482");
|
||||
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "38619d704068072a4ccfd354652957a2");
|
||||
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "bf64ab634126382813a6a6b29a5f47d8");
|
||||
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "be087f53429974b4e505cd59f9363bfe");
|
||||
expectations.put("-L 1:1-10000 --printPerLocus", "eb5802e7e615fa79b788a9447b7e824c");
|
||||
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "f4580866bcff10e0e742f422c45695d3");
|
||||
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "85c949c985d8aa340030362ea1fc13d2");
|
||||
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "a45430cfed2f574fb69e79d74ed41017");
|
||||
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "105547f432744e0776bd58e753cfa859");
|
||||
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "d758adbab9011e42c77d502fe4d62c27");
|
||||
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "933ec8327192c5ed58a1952c73fb4f73");
|
||||
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "7d5d0283d92220ee78db7465d675b37f");
|
||||
|
|
|
|||
Loading…
Reference in New Issue