First fully functional (though preliminary) version of walker that takes an input VCF and outputs a Beagle .bgl file that can be used for missing genotype calls/haplotype imputation. For now, only supported input format is likelihood format for unrelated individuals.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3444 348d0f76-0448-11de-a6fe-93d51630548a
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.oneoffprojects.walkers;
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import org.broad.tribble.vcf.VCFCodec;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.ArgumentCollection;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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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.variantcontext.Allele;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
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import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
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import java.io.PrintStream;
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import java.util.*;
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/**
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* Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input VCF fiel
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*/
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public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
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@Argument(fullName = "beagle_file", shortName = "beagle", doc = "File to print BEAGLE-specific data for use with imputation", required = false)
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public PrintStream beagleWriter = null;
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final TreeSet<String> samples = new TreeSet<String>();
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public void initialize() {
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final List<ReferenceOrderedDataSource> dataSources = this.getToolkit().getRodDataSources();
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for ( final ReferenceOrderedDataSource source : dataSources ) {
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final RMDTrack rod = source.getReferenceOrderedData();
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if ( rod.getType().equals(VCFCodec.class) ) {
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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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if ( beagleWriter != null ) {
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beagleWriter.print("marker alleleA alleleB");
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for ( String sample : samples )
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beagleWriter.print(String.format(" %s %s %s", sample, sample, sample));
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beagleWriter.println();
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}
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}
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public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
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if( tracker != null ) {
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EnumSet<VariantContext.Type> vc = EnumSet.of(VariantContext.Type.SNP);
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GenomeLoc loc = context.getLocation();
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VariantContext vc_eval;
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try {
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vc_eval = tracker.getVariantContext(ref,"eval", vc, loc, true);
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} catch (java.util.NoSuchElementException e) {
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return 0;
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}
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// output marker ID to Beagle input file
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beagleWriter.print(String.format("%s ",vc_eval.getLocation().toString()));
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for (Allele allele: vc_eval.getAlleles()) {
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// TODO -- check whether this is really needed by Beagle
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String bglPrintString;
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if (allele.isNoCall() || allele.isNull())
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bglPrintString = "0";
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else
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bglPrintString = allele.toString().substring(0,1); // get rid of * in case of reference allele
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beagleWriter.print(String.format("%s ", bglPrintString));
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}
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Map<String, Genotype> genotypes = vc_eval.getGenotypes();
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if ( genotypes == null || genotypes.size() == 0 )
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return null;
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for ( String sample : samples ) {
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// use sample as key into genotypes structure
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Genotype genotype = genotypes.get(sample);
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String gls = "0 0 0 ";
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if (genotype.isCalled()) {
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String[] glArray = genotype.getAttributeAsString("GL").split(",");
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for (String gl : glArray) {
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Double d_gl = -Double.valueOf(gl);
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beagleWriter.print(String.format("%5.2f ",d_gl));
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}
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}
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else
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beagleWriter.print(gls); // write 0 likelihoods for uncalled genotypes.
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}
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beagleWriter.println();
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}
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return 1;
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}
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public Integer reduceInit() {
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return 0; // Nothing to do here
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}
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public Integer reduce( Integer value, Integer sum ) {
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return 0; // Nothing to do here
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}
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public void onTraversalDone( Integer sum ) {
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}
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}
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