Updated. Now uses VariantContext and is truly "variants" to vcf (i.e. not just GELI to vcf).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3074 348d0f76-0448-11de-a6fe-93d51630548a
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@ -1,202 +1,72 @@
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package org.broadinstitute.sting.playground.gatk.walkers.variantstovcf;
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import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
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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.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.RodGeliText;
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import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
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import org.broadinstitute.sting.gatk.walkers.RefWalker;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.utils.genotype.Genotype;
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import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
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import org.broadinstitute.sting.utils.genotype.Variation;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.refdata.*;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RMD;
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import org.broadinstitute.sting.utils.genotype.vcf.*;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import java.io.File;
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import java.io.PrintStream;
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import java.util.*;
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/**
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* Converts variants from other file formats (anything that implements the Variation interface) to VCF format.
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* Converts variants from other file formats to VCF format.
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*/
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public class VariantsToVCF extends RefWalker<Integer, Integer> {
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@Argument(fullName="vcfout", shortName="VO", doc="The output VCF file") public File VCF_OUT;
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@Argument(fullName="verbose", shortName="V", doc="Show extended output", required=false) public boolean VERBOSE = false;
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@Argument(fullName="suppress_multistate_alleles", shortName="SMA", doc="When multi-sample genotypes imply something other than a biallele state, suppress it.", required=false) public boolean SUPPRESS_MULTISTATE = false;
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@Requires(value={},referenceMetaData=@RMD(name="variant",type= ReferenceOrderedDatum.class))
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public class VariantsToVCF extends RodWalker<Integer, Integer> {
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@Argument(fullName="sample", shortName="sample", doc="The sample name represented by the variant rod (for data like GELI with genotypes)", required=false)
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protected String sampleName = null;
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private VCFWriter vcfwriter = null;
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private VCFHeader vcfheader = null;
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private TreeMap<String, String> sampleNames = null;
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private static String format = "GT:GQ:DP";
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public void initialize() {
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sampleNames = new TreeMap<String, String>();
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GATKArgumentCollection args = this.getToolkit().getArguments();
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// Don't allow mixed types for now
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private EnumSet<VariantContext.Type> ALLOWED_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP, VariantContext.Type.NO_VARIATION, VariantContext.Type.INDEL);
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for (String rodName : args.RODBindings) {
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//out.println(rodName);
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String[] rodPieces = rodName.split(",");
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String sampleName = rodPieces[0];
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if (! ( sampleName.equals("dbSNP") || sampleName.equals("interval") ) ) {
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sampleNames.put(sampleName, sampleName);
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}
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}
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vcfheader = getHeader(args, sampleNames.keySet());
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vcfwriter = new VCFWriter(VCF_OUT);
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vcfwriter.writeHeader(vcfheader);
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}
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public static VCFHeader getHeader(GATKArgumentCollection args, Set<String> sampleNames) {
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// Don't output the data for now because it kills our unit test MD5s and is optional
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// TODO - figure out what to do here
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//Calendar cal = Calendar.getInstance();
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//metaData.put("fileDate", String.format("%d%02d%02d", cal.get(Calendar.YEAR), cal.get(Calendar.MONTH), cal.get(Calendar.DAY_OF_MONTH)));
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Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
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metaData.add(new VCFHeaderLine("source", "VariantsToVCF"));
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metaData.add(new VCFHeaderLine("reference", args.referenceFile.getAbsolutePath()));
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Set<String> additionalColumns = new HashSet<String>();
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additionalColumns.add("FORMAT");
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additionalColumns.addAll(sampleNames);
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return new VCFHeader(metaData, additionalColumns);
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}
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public boolean filter(RefMetaDataTracker tracker, char ref, AlignmentContext context) {
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if (BaseUtils.simpleBaseToBaseIndex(ref) > -1) {
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return true;
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}
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for (ReferenceOrderedDatum rod : tracker.getAllRods()) {
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if (rod != null && sampleNames.keySet().contains(rod.getName().toUpperCase())) {
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return true;
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}
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}
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return false;
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}
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private String[] ALLOWED_FORMAT_FIELDS = {"GT"};
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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List<VCFGenotypeRecord> gt = new ArrayList<VCFGenotypeRecord>();
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Map<VCFHeader.HEADER_FIELDS, String> map = new HashMap<VCFHeader.HEADER_FIELDS, String>();
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VCFRecord rec = generateVCFRecord(tracker, ref, context, vcfheader, gt, map, sampleNames, out, SUPPRESS_MULTISTATE, VERBOSE);
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if (rec != null) {
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vcfwriter.addRecord(rec);
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return 1;
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if ( tracker == null )
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return 0;
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rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getTrackData("dbsnp", null));
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Collection<VariantContext> contexts = tracker.getVariantContexts("variant", ALLOWED_VARIANT_CONTEXT_TYPES, context.getLocation(), true, false);
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for ( VariantContext vc : contexts ) {
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VCFRecord vcf = VariantContextAdaptors.toVCF(vc, ref.getBase(), Arrays.asList(ALLOWED_FORMAT_FIELDS), false, false);
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if ( dbsnp != null )
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vcf.setID(dbsnp.getRS_ID());
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if ( sampleName != null && vcf.hasGenotypeData() && vcf.getGenotype("variant") != null )
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vcf.getGenotype("variant").setSampleName(sampleName);
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writeRecord(vcf);
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}
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return 0;
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return 1;
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}
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public static VCFRecord generateVCFRecord(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context,
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VCFHeader vcfheader, List<VCFGenotypeRecord> gt, Map<VCFHeader.HEADER_FIELDS, String> map,
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Map<String, String> sampleNamesToRods, PrintStream out, boolean SUPPRESS_MULTISTATE, boolean VERBOSE) {
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int[] alleleCounts = new int[4];
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int numSNPs = 0;
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int numRefs = 0;
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int[] alleleNames = {0, 1, 2, 3};
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double snpQual = 0.0;
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int refbase = BaseUtils.simpleBaseToBaseIndex(ref.getBase());
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List<VCFGenotypeEncoding> alts = new ArrayList<VCFGenotypeEncoding>();
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for (String name : vcfheader.getGenotypeSamples()) {
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ReferenceOrderedDatum rod = tracker.lookup(sampleNamesToRods.get(name), null);
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if (rod != null) {
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Variation av = (Variation) rod;
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String lod = String.format("%d", av.getNegLog10PError() > 99 ? 99 : (int) av.getNegLog10PError());
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int depth = 0;
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private void writeRecord(VCFRecord rec) {
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if ( vcfwriter == null ) {
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// setup the header fields
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Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
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hInfo.add(new VCFHeaderLine("source", "VariantFiltration"));
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hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
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if (rod instanceof RodGeliText) {
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RodGeliText rv = (RodGeliText) rod;
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depth = rv.depth;
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}
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if (!(rod instanceof VariantBackedByGenotype))
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throw new IllegalArgumentException("The passed in variant type must be backed by genotype data");
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Genotype genotype = ((VariantBackedByGenotype) rod).getCalledGenotype();
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List<VCFGenotypeEncoding> alleles = new ArrayList<VCFGenotypeEncoding>();
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for (char base : genotype.getBases().toCharArray()) {
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alleles.add(new VCFGenotypeEncoding(String.valueOf(base)));
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if (base != ref.getBase() && !alts.contains(String.valueOf(base))) alts.add(new VCFGenotypeEncoding(String.valueOf(base)));
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}
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int allele1 = BaseUtils.simpleBaseToBaseIndex(genotype.getBases().charAt(0));
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int allele2 = BaseUtils.simpleBaseToBaseIndex(genotype.getBases().charAt(1));
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if (allele1 >= 0 && allele1 != refbase) {
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alleleCounts[allele1]++;
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}
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if (allele2 >= 0 && allele2 != refbase) {
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alleleCounts[allele2]++;
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}
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Map<String, String> str = new HashMap<String, String>();
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str.put("GQ", lod);
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if (depth > 0) str.put("DP", String.valueOf(depth));
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vcfwriter = new VCFWriter(out);
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VCFGenotypeRecord rec = new VCFGenotypeRecord(name, alleles, VCFGenotypeRecord.PHASE.UNPHASED);
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for ( Map.Entry<String, String> entry : str.entrySet() )
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rec.setField(entry.getKey(), entry.getValue());
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gt.add(rec);
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TreeSet<String> samples = new TreeSet<String>();
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if ( sampleName != null )
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samples.add(sampleName);
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else
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samples.addAll(Arrays.asList(rec.getSampleNames()));
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numSNPs++;
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snpQual += av.getNegLog10PError();
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} else if (BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1) {
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List<VCFGenotypeEncoding> alleles = new ArrayList<VCFGenotypeEncoding>();
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alleles.add(new VCFGenotypeEncoding(String.valueOf(ref.getBase())));
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alleles.add(new VCFGenotypeEncoding(String.valueOf(ref.getBase())));
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gt.add(new VCFGenotypeRecord(name, alleles, VCFGenotypeRecord.PHASE.UNPHASED));
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vcfwriter.writeHeader(new VCFHeader(hInfo, samples));
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numRefs++;
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}
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}
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if (numSNPs == 0)
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return null;
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Integer[] perm = Utils.SortPermutation(alleleCounts);
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int[] sortedCounts = Utils.PermuteArray(alleleCounts, perm);
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int[] sortedNames = Utils.PermuteArray(alleleNames, perm);
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rodDbSNP dbsnp = (rodDbSNP) tracker.lookup("dbsnp", null);
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String infoString = String.format("locus=%s ref=%c allele_count=( %c:%d %c:%d %c:%d %c:%d )",
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context.getLocation(),
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ref.getBase(),
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BaseUtils.baseIndexToSimpleBase(sortedNames[0]), sortedCounts[0],
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BaseUtils.baseIndexToSimpleBase(sortedNames[1]), sortedCounts[1],
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BaseUtils.baseIndexToSimpleBase(sortedNames[2]), sortedCounts[2],
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BaseUtils.baseIndexToSimpleBase(sortedNames[3]), sortedCounts[3]
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);
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if (SUPPRESS_MULTISTATE && sortedCounts[2] > 0) {
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out.println("[multistate] " + infoString);
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return null;
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} else {
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if (VERBOSE) {
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out.println("[locus_info] " + infoString);
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}
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}
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Map<String,String> info = new HashMap<String,String>();
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if (dbsnp != null) info.put("DB","1");
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if (dbsnp != null && dbsnp.isHapmap()) info.put("H2","1");
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return new VCFRecord(Character.toString(ref.getBase()),
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context.getContig(),
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(int) context.getPosition(),
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(dbsnp == null) ? "." : dbsnp.getRS_ID(),
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alts,
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snpQual > 99 ? 99 : (int) snpQual,
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"0",
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info,
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format,
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gt);
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vcfwriter.addRecord(rec);
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}
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public Integer reduceInit() {
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@ -208,8 +78,6 @@ public class VariantsToVCF extends RefWalker<Integer, Integer> {
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}
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public void onTraversalDone(Integer sum) {
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out.println("Processed " + sum + " variants.");
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vcfwriter.close();
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}
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}
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@ -5,7 +5,6 @@ import org.junit.Test;
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import java.util.List;
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import java.util.ArrayList;
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import java.io.File;
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/**
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@ -18,62 +17,38 @@ import java.io.File;
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public class VariantsToVCFIntegrationTest extends WalkerTest {
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//@Test
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@Test
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public void testVariantsToVCFUsingGeliInput() {
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List<String> md5 = new ArrayList<String>();
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md5.add("a94c15f2e8905fd3e98301375cf0f42a");
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md5.add("8f32f0efed5d0233cf9292198f4f01d8");
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/**
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* the above MD5 was calculated from running the following command:
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*
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* java -jar ./dist/GenomeAnalysisTK.jar \
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* -R /broad/1KG/reference/human_b36_both.fasta \
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* -T VariantEval \
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* --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod \
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* -L 1:10,000,000-11,000,000 \
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* --outerr myVariantEval \
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* --supressDateInformation \
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* --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls
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*
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*/
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-R " + oneKGLocation + "reference/human_b36_both.fasta" +
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" --rodBind NA123AB,Variants," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
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" -B variant,Variants," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
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" -T VariantsToVCF" +
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" -L 1:10,000,000-11,000,000" +
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" --vcfout %s",
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" -sample NA123AB" +
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" -o %s",
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1, // just one output file
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md5);
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List<File> result = executeTest("testVariantsToVCFUsingGeliInput", spec).getFirst();
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executeTest("testVariantsToVCFUsingGeliInput #1", spec).getFirst();
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}
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//@Test
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@Test
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public void testGenotypesToVCFUsingGeliInput() {
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List<String> md5 = new ArrayList<String>();
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md5.add("6b18f33e25edbd2154c17a949656644b");
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md5.add("40cc4d04d9a50043ce1322ea2650c453");
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/**
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* the above MD5 was calculated from running the following command:
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*
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* java -jar ./dist/GenomeAnalysisTK.jar \
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* -R /broad/1KG/reference/human_b36_both.fasta \
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* -T VariantEval \
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* --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod \
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* -L 1:10,000,000-11,000,000 \
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* --outerr myVariantEval \
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* --supressDateInformation \
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* --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls
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*
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*/
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-R " + oneKGLocation + "reference/human_b36_both.fasta" +
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" --rodBind NA123AB,Variants," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" +
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" -B variant,Variants," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" +
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" -T VariantsToVCF" +
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" -L 1:10,000,000-11,000,000" +
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" --vcfout %s",
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" -sample NA123AB" +
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" -o %s",
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1, // just one output file
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md5);
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List<File> result = executeTest("testVariantsToVCFUsingGeliInput", spec).getFirst();
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executeTest("testVariantsToVCFUsingGeliInput #2", spec).getFirst();
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}
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}
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