No longer uses VCFRecord
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3763 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
f130d29318
commit
0c4a32843c
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@ -428,4 +428,9 @@ public class VariantContextUtils {
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public static String mergedSampleName(String trackName, String sampleName, boolean uniqify ) {
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public static String mergedSampleName(String trackName, String sampleName, boolean uniqify ) {
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return uniqify ? sampleName + "." + trackName : sampleName;
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return uniqify ? sampleName + "." + trackName : sampleName;
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}
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}
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public static VariantContext modifyAttributes(VariantContext vc, Map<String, Object> attributes) {
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return new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.getFilters(), attributes);
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}
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}
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}
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@ -25,23 +25,20 @@
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package org.broadinstitute.sting.playground.gatk.walkers;
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package org.broadinstitute.sting.playground.gatk.walkers;
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import org.broad.tribble.vcf.*;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
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import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
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import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
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import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.gatk.walkers.RMD;
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import org.broadinstitute.sting.gatk.walkers.RMD;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
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import org.broad.tribble.vcf.*;
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import java.io.*;
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import java.io.*;
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import java.util.*;
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import java.util.*;
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@ -51,11 +48,11 @@ import static java.lang.Math.log10;
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/**
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/**
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* Takes files produced by Beagle imputation engine and creates a vcf with modified annotations.
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* Takes files produced by Beagle imputation engine and creates a vcf with modified annotations.
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*/
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*/
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@Requires(value={},referenceMetaData=@RMD(name=BeagleOutputToVCFWalker.INPUT_ROD_NAME,type= VCFRecord.class))
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@Requires(value={},referenceMetaData=@RMD(name=BeagleOutputToVCFWalker.INPUT_ROD_NAME, type=ReferenceOrderedDatum.class))
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public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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private VCFWriter vcfWriter;
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public static final String INPUT_ROD_NAME = "variant";
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@Argument(fullName="output_file", shortName="output", doc="VCF file to which output should be written", required=true)
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@Argument(fullName="output_file", shortName="output", doc="VCF file to which output should be written", required=true)
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private String OUTPUT_FILE = null;
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private String OUTPUT_FILE = null;
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@ -63,45 +60,33 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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@Argument(fullName="nocall_threshold", shortName="ncthr", doc="Threshold of confidence at which a genotype won't be called", required=false)
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@Argument(fullName="nocall_threshold", shortName="ncthr", doc="Threshold of confidence at which a genotype won't be called", required=false)
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private double noCallThreshold = 0.0;
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private double noCallThreshold = 0.0;
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public static final String INPUT_ROD_NAME = "inputvcf";
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protected static String line = null;
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protected static String line = null;
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private VCFWriter vcfWriter;
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// protected HashMap<String,BeagleSampleRecord> beagleSampleRecords;
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// protected HashMap<String,BeagleSampleRecord> beagleSampleRecords;
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final TreeSet<String> samples = new TreeSet<String>();
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TreeSet<String> samples = null;
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private final double MIN_PROB_ERROR = 0.000001;
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private final double MIN_PROB_ERROR = 0.000001;
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private final double MAX_GENOTYPE_QUALITY = 6.0;
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private final double MAX_GENOTYPE_QUALITY = 6.0;
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public void initialize() {
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private void initialize(Set<String> sampleNames) {
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// setup the header fields
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// setup the header fields
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final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
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hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
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hInfo.add(new VCFFormatHeaderLine("OG",1,VCFHeaderLineType.String, "Original Genotype input to Beagle"));
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hInfo.add(new VCFFormatHeaderLine("OG",1, VCFHeaderLineType.String, "Original Genotype input to Beagle"));
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hInfo.add(new VCFInfoHeaderLine("R2", 1, VCFHeaderLineType.Float, "r2 Value reported by Beagle on each site"));
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hInfo.add(new VCFInfoHeaderLine("R2", 1, VCFHeaderLineType.Float, "r2 Value reported by Beagle on each site"));
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hInfo.add(new VCFInfoHeaderLine("GenotypesChanged", 1, VCFHeaderLineType.Flag, "r2 Value reported by Beagle on each site"));
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hInfo.add(new VCFInfoHeaderLine("GenotypesChanged", 1, VCFHeaderLineType.Flag, "r2 Value reported by Beagle on each site"));
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hInfo.add(new VCFHeaderLine("source", "BeagleImputation"));
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hInfo.add(new VCFHeaderLine("source", "BeagleImputation"));
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final List<ReferenceOrderedDataSource> dataSources = this.getToolkit().getRodDataSources();
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// Open output file specified by output VCF ROD
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// Open output file specified by output VCF ROD
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vcfWriter = new VCFWriter(new File(OUTPUT_FILE));
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vcfWriter = new VCFWriter(new File(OUTPUT_FILE));
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for( final ReferenceOrderedDataSource source : dataSources ) {
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samples = new TreeSet<String>(sampleNames);
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final RMDTrack rod = source.getReferenceOrderedData();
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if( rod.getRecordType().equals(VCFRecord.class) && rod.getName().equalsIgnoreCase(INPUT_ROD_NAME)) {
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final VCFReader reader = new VCFReader(rod.getFile());
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final Set<String> vcfSamples = reader.getHeader().getGenotypeSamples();
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samples.addAll(vcfSamples);
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reader.close();
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}
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}
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final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
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final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
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vcfWriter.writeHeader(vcfHeader);
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vcfWriter.writeHeader(vcfHeader);
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@ -110,155 +95,154 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
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public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
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if ( tracker == null )
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if ( tracker == null )
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return 0;
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return 0;
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GenomeLoc loc = context.getLocation();
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GenomeLoc loc = context.getLocation();
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VariantContext vc_input = tracker.getVariantContext(ref,"inputvcf", null, loc, false);
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VariantContext vc_input = tracker.getVariantContext(ref,"inputvcf", null, loc, false);
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if ( vc_input == null )
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if ( vc_input == null )
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return 0;
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return 0;
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if ( samples == null ) {
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initialize(vc_input.getSampleNames());
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}
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List<Object> r2rods = tracker.getReferenceMetaData("beagleR2");
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// ignore places where we don't have a variant
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if ( r2rods.size() == 0 )
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return 0;
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BeagleFeature beagleR2Feature = (BeagleFeature)r2rods.get(0);
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List<Object> gProbsrods = tracker.getReferenceMetaData("beagleProbs");
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// ignore places where we don't have a variant
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if ( gProbsrods.size() == 0 )
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return 0;
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BeagleFeature beagleProbsFeature = (BeagleFeature)gProbsrods.get(0);
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List<Object> gPhasedrods = tracker.getReferenceMetaData("beaglePhased");
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// ignore places where we don't have a variant
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if ( gPhasedrods.size() == 0 )
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return 0;
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BeagleFeature beaglePhasedFeature = (BeagleFeature)gPhasedrods.get(0);
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// get reference base for current position
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byte refByte = ref.getBase();
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// make new Genotypes based on Beagle results
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Map<String, Genotype> genotypes = new HashMap<String, Genotype>(vc_input.getGenotypes().size());
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List<Object> r2rods = tracker.getReferenceMetaData("beagleR2");
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// for each genotype, create a new object with Beagle information on it
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boolean genotypesChangedByBeagle = false;
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for ( Map.Entry<String, Genotype> originalGenotypes : vc_input.getGenotypes().entrySet() ) {
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// ignore places where we don't have a variant
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Genotype g = originalGenotypes.getValue();
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if ( r2rods.size() == 0 )
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Set<String> filters = new LinkedHashSet<String>(g.getFilters());
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return 0;
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BeagleFeature beagleR2Feature = (BeagleFeature)r2rods.get(0);
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boolean genotypeIsPhased = true;
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String sample = g.getSampleName();
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List<Object> gProbsrods = tracker.getReferenceMetaData("beagleProbs");
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ArrayList<String> beagleProbabilities = beagleProbsFeature.getProbLikelihoods().get(sample);
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ArrayList<String> beagleGenotypePairs = beaglePhasedFeature.getGenotypes().get(sample);
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// ignore places where we don't have a variant
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Allele originalAlleleA = g.getAllele(0);
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if ( gProbsrods.size() == 0 )
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Allele originalAlleleB = g.getAllele(1);
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return 0;
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BeagleFeature beagleProbsFeature = (BeagleFeature)gProbsrods.get(0);
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// We have phased genotype in hp. Need to set the isRef field in the allele.
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List<Allele> alleles = new ArrayList<Allele>();
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List<Object> gPhasedrods = tracker.getReferenceMetaData("beaglePhased");
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String alleleA = beagleGenotypePairs.get(0);
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String alleleB = beagleGenotypePairs.get(1);
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// ignore places where we don't have a variant
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byte[] r = alleleA.getBytes();
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if ( gPhasedrods.size() == 0 )
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byte rA = r[0];
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return 0;
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BeagleFeature beaglePhasedFeature = (BeagleFeature)gPhasedrods.get(0);
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Boolean isRefA = (refByte == rA);
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// get reference base for current position
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Allele refAllele = Allele.create(r, isRefA );
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byte refByte = ref.getBase();
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alleles.add(refAllele);
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// make new Genotypes based on Beagle results
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r = alleleB.getBytes();
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Map<String, Genotype> genotypes = new HashMap<String, Genotype>(vc_input.getGenotypes().size());
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byte rB = r[0];
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Boolean isRefB = (refByte == rB);
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Allele altAllele = Allele.create(r,isRefB);
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alleles.add(altAllele);
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// for each genotype, create a new object with Beagle information on it
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// Compute new GQ field = -10*log10Pr(Genotype call is wrong)
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boolean genotypesChangedByBeagle = false;
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// Beagle gives probability that genotype is AA, AB and BB.
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for ( Map.Entry<String, Genotype> originalGenotypes : vc_input.getGenotypes().entrySet() ) {
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// Which, by definition, are prob of hom ref, het and hom var.
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Double probWrongGenotype, genotypeQuality;
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Double homRefProbability = Double.valueOf(beagleProbabilities.get(0));
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Double hetProbability = Double.valueOf(beagleProbabilities.get(1));
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Double homVarProbability = Double.valueOf(beagleProbabilities.get(2));
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if (isRefA && isRefB) // HomRef call
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probWrongGenotype = hetProbability + homVarProbability;
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else if ((isRefB && !isRefA) || (isRefA && !isRefB))
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probWrongGenotype = homRefProbability + homVarProbability;
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else // HomVar call
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probWrongGenotype = hetProbability + homRefProbability;
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Genotype g = originalGenotypes.getValue();
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if (1-probWrongGenotype < noCallThreshold) {
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Set<String> filters = new LinkedHashSet<String>(g.getFilters());
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// quality is bad: don't call genotype
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alleles.clear();
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boolean genotypeIsPhased = true;
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refAllele = Allele.NO_CALL;
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String sample = g.getSampleName();
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altAllele = Allele.NO_CALL;
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alleles.add(refAllele);
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ArrayList<String> beagleProbabilities = beagleProbsFeature.getProbLikelihoods().get(sample);
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alleles.add(altAllele);
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ArrayList<String> beagleGenotypePairs = beaglePhasedFeature.getGenotypes().get(sample);
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genotypeIsPhased = false;
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Allele originalAlleleA = g.getAllele(0);
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Allele originalAlleleB = g.getAllele(1);
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// We have phased genotype in hp. Need to set the isRef field in the allele.
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List<Allele> alleles = new ArrayList<Allele>();
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String alleleA = beagleGenotypePairs.get(0);
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String alleleB = beagleGenotypePairs.get(1);
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byte[] r = alleleA.getBytes();
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byte rA = r[0];
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Boolean isRefA = (refByte == rA);
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Allele refAllele = Allele.create(r, isRefA );
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alleles.add(refAllele);
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r = alleleB.getBytes();
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byte rB = r[0];
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Boolean isRefB = (refByte == rB);
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Allele altAllele = Allele.create(r,isRefB);
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alleles.add(altAllele);
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// Compute new GQ field = -10*log10Pr(Genotype call is wrong)
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// Beagle gives probability that genotype is AA, AB and BB.
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// Which, by definition, are prob of hom ref, het and hom var.
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Double probWrongGenotype, genotypeQuality;
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Double homRefProbability = Double.valueOf(beagleProbabilities.get(0));
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Double hetProbability = Double.valueOf(beagleProbabilities.get(1));
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Double homVarProbability = Double.valueOf(beagleProbabilities.get(2));
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if (isRefA && isRefB) // HomRef call
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probWrongGenotype = hetProbability + homVarProbability;
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else if ((isRefB && !isRefA) || (isRefA && !isRefB))
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probWrongGenotype = homRefProbability + homVarProbability;
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else // HomVar call
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probWrongGenotype = hetProbability + homRefProbability;
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if (1-probWrongGenotype < noCallThreshold) {
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// quality is bad: don't call genotype
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alleles.clear();
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refAllele = Allele.NO_CALL;
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altAllele = Allele.NO_CALL;
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alleles.add(refAllele);
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alleles.add(altAllele);
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genotypeIsPhased = false;
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}
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if (probWrongGenotype < MIN_PROB_ERROR)
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genotypeQuality = MAX_GENOTYPE_QUALITY;
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else
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genotypeQuality = -log10(probWrongGenotype);
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HashMap<String,Object> originalAttributes = new HashMap<String,Object>(g.getAttributes());
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// get original encoding and add to keynotype attributes
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String a1, a2, og;
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if (originalAlleleA.isNoCall())
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a1 = ".";
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else if (originalAlleleA.isReference())
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a1 = "0";
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else
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a1 = "1";
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if (originalAlleleB.isNoCall())
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a2 = ".";
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else if (originalAlleleB.isReference())
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a2 = "0";
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else
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a2 = "1";
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og = a1+"/"+a2;
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// See if Beagle switched genotypes
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if (!((refAllele.equals(originalAlleleA) && altAllele.equals(originalAlleleB) ||
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(refAllele.equals(originalAlleleB) && altAllele.equals(originalAlleleA))))){
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genotypesChangedByBeagle = true;
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originalAttributes.put("OG",og);
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||||||
}
|
}
|
||||||
else {
|
|
||||||
originalAttributes.put("OG",".");
|
if (probWrongGenotype < MIN_PROB_ERROR)
|
||||||
}
|
genotypeQuality = MAX_GENOTYPE_QUALITY;
|
||||||
Genotype imputedGenotype = new Genotype(originalGenotypes.getKey(), alleles, genotypeQuality, filters,originalAttributes , genotypeIsPhased);
|
else
|
||||||
|
genotypeQuality = -log10(probWrongGenotype);
|
||||||
|
|
||||||
|
HashMap<String,Object> originalAttributes = new HashMap<String,Object>(g.getAttributes());
|
||||||
|
|
||||||
|
// get original encoding and add to keynotype attributes
|
||||||
|
String a1, a2, og;
|
||||||
|
if (originalAlleleA.isNoCall())
|
||||||
|
a1 = ".";
|
||||||
|
else if (originalAlleleA.isReference())
|
||||||
|
a1 = "0";
|
||||||
|
else
|
||||||
|
a1 = "1";
|
||||||
|
|
||||||
|
if (originalAlleleB.isNoCall())
|
||||||
|
a2 = ".";
|
||||||
|
else if (originalAlleleB.isReference())
|
||||||
|
a2 = "0";
|
||||||
|
else
|
||||||
|
a2 = "1";
|
||||||
|
|
||||||
|
og = a1+"/"+a2;
|
||||||
|
|
||||||
|
// See if Beagle switched genotypes
|
||||||
|
if (!((refAllele.equals(originalAlleleA) && altAllele.equals(originalAlleleB) ||
|
||||||
|
(refAllele.equals(originalAlleleB) && altAllele.equals(originalAlleleA))))){
|
||||||
|
genotypesChangedByBeagle = true;
|
||||||
|
originalAttributes.put("OG",og);
|
||||||
|
}
|
||||||
|
else {
|
||||||
|
originalAttributes.put("OG",".");
|
||||||
|
}
|
||||||
|
Genotype imputedGenotype = new Genotype(originalGenotypes.getKey(), alleles, genotypeQuality, filters,originalAttributes , genotypeIsPhased);
|
||||||
|
|
||||||
|
|
||||||
genotypes.put(originalGenotypes.getKey(), imputedGenotype);
|
genotypes.put(originalGenotypes.getKey(), imputedGenotype);
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
VariantContext filteredVC = new VariantContext("outputvcf", vc_input.getLocation(), vc_input.getAlleles(), genotypes, vc_input.getNegLog10PError(), vc_input.getFilters(), vc_input.getAttributes());
|
VariantContext filteredVC = new VariantContext("outputvcf", vc_input.getLocation(), vc_input.getAlleles(), genotypes, vc_input.getNegLog10PError(), vc_input.getFilters(), vc_input.getAttributes());
|
||||||
|
|
||||||
|
|
||||||
Set<Allele> altAlleles = filteredVC.getAlternateAlleles();
|
Set<Allele> altAlleles = filteredVC.getAlternateAlleles();
|
||||||
StringBuffer altAlleleCountString = new StringBuffer();
|
StringBuffer altAlleleCountString = new StringBuffer();
|
||||||
for ( Allele allele : altAlleles ) {
|
for ( Allele allele : altAlleles ) {
|
||||||
|
|
@ -267,22 +251,20 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
|
||||||
altAlleleCountString.append(filteredVC.getChromosomeCount(allele));
|
altAlleleCountString.append(filteredVC.getChromosomeCount(allele));
|
||||||
}
|
}
|
||||||
|
|
||||||
VCFRecord vcf = VariantContextAdaptors.toVCF(filteredVC, ref.getBase());
|
HashMap<String, Object> attributes = new HashMap<String, Object>(filteredVC.getAttributes());
|
||||||
|
|
||||||
if ( filteredVC.getChromosomeCount() > 0 ) {
|
if ( filteredVC.getChromosomeCount() > 0 ) {
|
||||||
vcf.addInfoField(VCFConstants.ALLELE_NUMBER_KEY, String.format("%d", filteredVC.getChromosomeCount()));
|
attributes.put(VCFConstants.ALLELE_NUMBER_KEY, String.format("%d", filteredVC.getChromosomeCount()));
|
||||||
if ( altAlleleCountString.length() > 0 ) {
|
if ( altAlleleCountString.length() > 0 ) {
|
||||||
vcf.addInfoField(VCFConstants.ALLELE_COUNT_KEY, altAlleleCountString.toString());
|
attributes.put(VCFConstants.ALLELE_COUNT_KEY, altAlleleCountString.toString());
|
||||||
vcf.addInfoField(VCFConstants.ALLELE_FREQUENCY_KEY, String.format("%4.2f",
|
attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, String.format("%4.2f",
|
||||||
Double.valueOf(altAlleleCountString.toString())/(filteredVC.getChromosomeCount())));
|
Double.valueOf(altAlleleCountString.toString())/(filteredVC.getChromosomeCount())));
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
attributes.put("GenotypesChanged", (genotypesChangedByBeagle)? "1":"0" );
|
||||||
|
attributes.put("R2", beagleR2Feature.getR2value().toString() );
|
||||||
|
|
||||||
vcf.addInfoField("GenotypesChanged", (genotypesChangedByBeagle)? "1":"0" );
|
vcfWriter.add(VariantContextUtils.modifyAttributes(filteredVC, attributes), new byte[]{ref.getBase()});
|
||||||
vcf.addInfoField("R2", beagleR2Feature.getR2value().toString() );
|
|
||||||
vcfWriter.addRecord(vcf);
|
|
||||||
|
|
||||||
|
|
||||||
return 1;
|
return 1;
|
||||||
|
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue