124 lines
5.6 KiB
Java
Executable File
124 lines
5.6 KiB
Java
Executable File
package org.broadinstitute.sting.playground.gatk.walkers;
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import net.sf.samtools.SAMRecord;
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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.Genotype;
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import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.VariationRod;
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import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper;
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import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Set;
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/**
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* Implements a rudimentary algorithm for calling SNPs that are de novo in that they appear in an individual but not in
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* its parents.
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*/
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@By(DataSource.REFERENCE)
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@Requires(value={DataSource.REFERENCE, DataSource.REFERENCE_BASES, DataSource.READS},referenceMetaData={@RMD(name="child",type= VariationRod.class)})
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@Allows({DataSource.READS, DataSource.REFERENCE})
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@ReadFilters(ZeroMappingQualityReadFilter.class)
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//, @RMD(name="parent1",type= VariationRod.class), @RMD(name="parent2",type= VariationRod.class)})
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public class DeNovoSNPWalker extends RefWalker<String, Integer>{
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/**
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* Implements a rudimentary algorithm for calling SNPs that are de novo in that they appear in an individual but not in
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* its parents. Using BAM files corresponding to parents and child, it calls UnifiedGenotyper directly and outputs a
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* confidence for positions being de novo SNPs.
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* */
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UnifiedGenotyper UG;
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private List<Set<String>> readGroupSets;
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public void initialize() {
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UG = new UnifiedGenotyper();
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UG.initialize();
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readGroupSets = getToolkit().getMergedReadGroupsByReaders();
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}
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public String map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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VariationRod child = tracker.lookup("child",VariationRod.class);
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VariationRod dbsnp = tracker.lookup(rodDbSNP.STANDARD_DBSNP_TRACK_NAME,VariationRod.class);
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if (child != null) {
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if (child.isSNP() && child.getNegLog10PError() > 5) { // BTR > 5
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List<SAMRecord> reads = context.getReads();
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List<Integer> offsets = context.getOffsets();
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List<SAMRecord> parent1_reads = new ArrayList<SAMRecord>();
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List<SAMRecord> parent2_reads = new ArrayList<SAMRecord>();
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List<Integer> parent1_offsets = new ArrayList<Integer>();
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List<Integer> parent2_offsets = new ArrayList<Integer>();
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assert( reads.size() == offsets.size() ); // should be same number or we're in trouble
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int num_reads = reads.size();
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for (int i=0; i<num_reads; i++) {
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SAMRecord read = reads.get(i);
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Integer offset = offsets.get(i);
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String readGroup = (String)read.getAttribute("RG");
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if (readGroupSets.get(0).contains(readGroup)) {
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parent1_reads.add(read);
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parent1_offsets.add(offset);
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} else if (readGroupSets.get(1).contains(readGroup)) {
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parent2_reads.add(read);
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parent2_offsets.add(offset);
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}
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}
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AlignmentContext parent1_subContext = new AlignmentContext(context.getLocation(), parent1_reads, parent1_offsets);
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VariantCallContext parent1 = UG.map(tracker, ref, parent1_subContext);
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AlignmentContext parent2_subContext = new AlignmentContext(context.getLocation(), parent2_reads, parent2_offsets);
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VariantCallContext parent2 = UG.map(tracker, ref, parent2_subContext);
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if ( parent1 != null && parent1.vc != null && parent2 != null && parent2.vc != null ) {
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Genotype parent1call = parent1.vc.getGenotype(0);
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Genotype parent2call = parent2.vc.getGenotype(0);
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if (parent1call.isHomRef() &&
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parent1call.getNegLog10PError() > 5 &&
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!parent2call.isHomRef() &&
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parent2call.getNegLog10PError() > 5) {
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double sumConfidences = 0.5 * (0.5 * child.getNegLog10PError() +
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Math.min(parent1call.getNegLog10PError(), parent2call.getNegLog10PError()));
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out.format("%s\t", child.getLocation().getContig());
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out.format("%s\t", child.getLocation().getStart());
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out.format("%.4f\t", sumConfidences);
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out.format("%.4f\t", child.getNegLog10PError());
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out.format("%.4f\t", parent1call.getNegLog10PError());
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out.format("%.4f\t", parent2call.getNegLog10PError());
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out.format("%s\t", dbsnp != null);
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out.format ("%s\t", child.toString());
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out.format ("%s\t", parent1.toString());
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out.format ("%s", parent2.toString());
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if (dbsnp != null)
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out.format ("\tDBSNP\t:%s", dbsnp.toString());
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out.println();
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}
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}
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}
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}
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return "";
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}
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public Integer reduceInit() { return 0; }
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public Integer reduce(String line, Integer a) {
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return 1;
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}
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public void onTraversalDone(Integer result) {} // Don't print the reduce result
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}
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