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* new LocusDepthtoBAF tool * tests * address reviewer comments * prohibit multi-allelic sites
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src/main/java/org/broadinstitute/hellbender/tools/sv/LocusDepthtoBAF.java
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| package org.broadinstitute.hellbender.tools.sv; | ||
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| import com.google.common.annotations.VisibleForTesting; | ||
| import htsjdk.samtools.SAMSequenceDictionary; | ||
| import htsjdk.samtools.util.Locatable; | ||
| import htsjdk.tribble.Feature; | ||
| import htsjdk.variant.variantcontext.Allele; | ||
| import htsjdk.variant.variantcontext.VariantContext; | ||
| import org.apache.commons.math3.distribution.ChiSquaredDistribution; | ||
| import org.broadinstitute.barclay.argparser.Argument; | ||
| import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; | ||
| import org.broadinstitute.barclay.argparser.ExperimentalFeature; | ||
| import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; | ||
| import org.broadinstitute.hellbender.cmdline.programgroups.StructuralVariantDiscoveryProgramGroup; | ||
| import org.broadinstitute.hellbender.engine.*; | ||
| import org.broadinstitute.hellbender.exceptions.UserException; | ||
| import org.broadinstitute.hellbender.utils.MathUtils.RunningAverage; | ||
| import org.broadinstitute.hellbender.utils.Nucleotide; | ||
| import org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodec; | ||
| import org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodecFinder; | ||
| import org.broadinstitute.hellbender.utils.codecs.FeatureSink; | ||
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|
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| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.Iterator; | ||
| import java.util.List; | ||
|
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| /** | ||
| * <p>Merges locus-sorted LocusDepth evidence files, and calculates the bi-allelic frequency (baf) | ||
| * for each sample and site, and writes these values as a BafEvidence output file.</p> | ||
| * <p>Samples at sites that have too few depth counts (controlled by --min-total-depth), and samples | ||
| * failing a Pearson's chi square test for goodness of fit to a bi-allelic model are excluded. (I.e., | ||
| * only samples that are judged to be heterozygous at a site are included.)</p> | ||
| * <p>Across all evaluable samples, sites where the samples have bafs with too much variance | ||
| * (controlled by --max-std) are excluded. The median baf value at each site is adjusted to be | ||
| * exactly 0.5.</p> | ||
| * | ||
| * <h3>Inputs</h3> | ||
| * | ||
| * <ul> | ||
| * <li> | ||
| * One or more LocusDepth evidence files, or a file containing a list of evidence files, one per line. | ||
| * </li> | ||
| * </ul> | ||
| * | ||
| * <h3>Output</h3> | ||
| * | ||
| * <ul> | ||
| * <li> | ||
| * An output file containing merged BafEvidence from the inputs. | ||
| * </li> | ||
| * </ul> | ||
| * | ||
| * <h3>Usage example</h3> | ||
| * | ||
| * <pre> | ||
| * gatk LocusDepthtoBAF \ | ||
| * -F file1.ld.txt.gz [-F file2.ld.txt.gz ...] \ | ||
| * -O merged.baf.bci | ||
| * </pre> | ||
| * | ||
| * @author Ted Sharpe <[email protected]> | ||
| */ | ||
| @CommandLineProgramProperties( | ||
| summary = "Convert LocusDepth to BafEvidence", | ||
| oneLineSummary = "Convert LocusDepth to BafEvidence", | ||
| programGroup = StructuralVariantDiscoveryProgramGroup.class | ||
| ) | ||
| @ExperimentalFeature | ||
| public class LocusDepthtoBAF extends MultiFeatureWalker<LocusDepth> { | ||
| public static final String LOCUS_DEPTH_FILE_NAME = "locus-depth"; | ||
| public static final String BAF_SITES_VCF_LONG_NAME = "baf-sites-vcf"; | ||
| public static final String SAMPLE_NAMES_NAME = "sample-names"; | ||
| public static final String BAF_EVIDENCE_FILE_NAME = "baf-evidence-output"; | ||
| public static final String MIN_TOTAL_DEPTH_NAME = "min-total-depth"; | ||
| public static final String MAX_STD_NAME = "max-std"; | ||
| public static final String MIN_HET_PROBABILITY = "min-het-probability"; | ||
| public static final String COMPRESSION_LEVEL_NAME = "compression-level"; | ||
| public static ChiSquaredDistribution chiSqDist = new ChiSquaredDistribution(null, 1.); | ||
|
|
||
| @Argument( | ||
| doc = "Locus depth files to process", | ||
| fullName = LOCUS_DEPTH_FILE_NAME, | ||
| shortName = StandardArgumentDefinitions.FEATURE_SHORT_NAME ) | ||
| private List<FeatureInput<LocusDepth>> locusDepthFiles; | ||
|
|
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| @Argument(fullName = BAF_SITES_VCF_LONG_NAME, | ||
| doc = "Input VCF of SNPs marking loci for allele counts") | ||
| public GATKPath bafSitesFile; | ||
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|
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| @Argument(fullName = SAMPLE_NAMES_NAME, | ||
| doc = "Sample names. Necessary only when writing a *.baf.bci output file.", optional = true) | ||
| private List<String> sampleNames; | ||
|
|
||
| @Argument( | ||
| doc = "BAF output file", | ||
| fullName = BAF_EVIDENCE_FILE_NAME, | ||
| shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME ) | ||
| private GATKPath bafOutputFile; | ||
|
|
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| @Argument( | ||
| doc = "Maximum standard deviation across bafs at a locus (otherwise locus will be ignored)", | ||
| fullName = MAX_STD_NAME, optional = true ) | ||
| private double maxStdDev = .2; | ||
|
|
||
| @Argument( | ||
| doc = "Minimum total depth at a locus (otherwise locus will be ignored)", | ||
| fullName = MIN_TOTAL_DEPTH_NAME, optional = true ) | ||
| private int minTotalDepth = 10; | ||
|
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| @Argument( | ||
| doc = "Minimum probability of site being biallelic and heterozygous", | ||
| fullName = MIN_HET_PROBABILITY, optional = true ) | ||
| private double minHetProbability = .5; | ||
|
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| @Argument( | ||
| doc = "Output compression level", | ||
| fullName = COMPRESSION_LEVEL_NAME, | ||
| minValue = 0, maxValue = 9, optional = true ) | ||
| private int compressionLevel = 4; | ||
|
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| private FeatureDataSource<VariantContext> bafSitesSource; | ||
| private Iterator<VariantContext> bafSitesIterator; | ||
| private FeatureSink<BafEvidence> writer; | ||
| private final List<LocusDepth> sameLocusBuffer = new ArrayList<>(); | ||
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| @Override | ||
| @SuppressWarnings("unchecked") | ||
| public void onTraversalStart() { | ||
| super.onTraversalStart(); | ||
| bafSitesSource = new FeatureDataSource<>(bafSitesFile.toPath().toString()); | ||
| bafSitesIterator = bafSitesSource.iterator(); | ||
| final SAMSequenceDictionary dict = getDictionary(); | ||
| dict.assertSameDictionary(bafSitesSource.getSequenceDictionary()); | ||
| final FeatureOutputCodec<? extends Feature, ? extends FeatureSink<? extends Feature>> codec = | ||
| FeatureOutputCodecFinder.find(bafOutputFile); | ||
| if ( !codec.getFeatureType().isAssignableFrom(BafEvidence.class) ) { | ||
| throw new UserException("We're intending to write BafEvidence, but the feature type " + | ||
| "associated with the output file expects features of type " + | ||
| codec.getFeatureType().getSimpleName()); | ||
| } | ||
| writer = (FeatureSink<BafEvidence>)codec.makeSink(bafOutputFile, dict, sampleNames, | ||
| compressionLevel); | ||
| } | ||
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| @Override | ||
| public void apply( final LocusDepth locusDepth, final Object header, | ||
| final ReadsContext reads, final ReferenceContext ref ) { | ||
| if ( !sameLocus(locusDepth) ) { | ||
| processBuffer(); | ||
| } | ||
| sameLocusBuffer.add(locusDepth); | ||
| } | ||
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||
| @Override | ||
| public Object onTraversalSuccess() { | ||
| super.onTraversalSuccess(); | ||
| if ( !sameLocusBuffer.isEmpty() ) { | ||
| processBuffer(); | ||
| } | ||
| bafSitesSource.close(); | ||
| writer.close(); | ||
| return null; | ||
| } | ||
|
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| /** Performs a Pearson's chi square test for goodness of fit to a biallelic model to determine | ||
| * heterozygosity. If this fails, BafEvidence.MISSING_VALUE is returned. If the test succeeds, | ||
| * the depth of the alt call as a fraction of the total depth is returned. | ||
| */ | ||
| @VisibleForTesting double calcBAF( final LocusDepth locusDepth, | ||
| final int refIndex, final int altIndex ) { | ||
| final int totalDepth = locusDepth.getTotalDepth(); | ||
| if ( totalDepth < minTotalDepth ) { | ||
| return BafEvidence.MISSING_VALUE; | ||
| } | ||
| final double expectRefAlt = totalDepth / 2.; | ||
| final double altDepth = locusDepth.getDepth(altIndex); | ||
| final double refDiff = locusDepth.getDepth(refIndex) - expectRefAlt; | ||
| final double altDiff = altDepth - expectRefAlt; | ||
| final double chiSq = (refDiff * refDiff + altDiff * altDiff) / expectRefAlt; | ||
| final double fitProb = 1. - chiSqDist.cumulativeProbability(chiSq); | ||
| if ( fitProb < minHetProbability ) { | ||
| return BafEvidence.MISSING_VALUE; | ||
| } | ||
| return altDepth / totalDepth; | ||
| } | ||
|
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| private boolean sameLocus( final Locatable locus ) { | ||
| if ( sameLocusBuffer.isEmpty() ) { | ||
| return true; | ||
| } | ||
| final LocusDepth curLocus = sameLocusBuffer.get(0); | ||
| return curLocus.getContig().equals(locus.getContig()) && | ||
| curLocus.getStart() == locus.getStart(); | ||
| } | ||
|
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| private void processBuffer() { | ||
| final VariantContext vc = nextSite(); | ||
| if ( !sameLocus(vc) ) { | ||
| final Locatable loc = sameLocusBuffer.get(0); | ||
| throw new UserException("expecting locus " + loc.getContig() + ":" + loc.getStart() + | ||
| ", but found locus " + vc.getContig() + ":" + vc.getStart() + " in baf sites vcf"); | ||
| } | ||
| final List<Allele> alleles = vc.getAlleles(); | ||
| final int refIndex = Nucleotide.decode(alleles.get(0).getBases()[0]).ordinal(); | ||
| if ( refIndex > 3 ) { | ||
| throw new UserException("ref call is not [ACGT] in vcf at " + vc.getContig() + ":" + vc.getStart()); | ||
| } | ||
| final int altIndex = Nucleotide.decode(alleles.get(1).getBases()[0]).ordinal(); | ||
| if ( altIndex > 3 ) { | ||
| throw new UserException("alt call is not [ACGT] in vcf at " + vc.getContig() + ":" + vc.getStart()); | ||
| } | ||
| final List<BafEvidence> beList = new ArrayList<>(sameLocusBuffer.size()); | ||
| for ( final LocusDepth ld : sameLocusBuffer ) { | ||
| final double baf = calcBAF(ld, refIndex, altIndex); | ||
| if ( baf != BafEvidence.MISSING_VALUE ) { | ||
| beList.add(new BafEvidence(ld.getSample(), ld.getContig(), ld.getStart(), baf)); | ||
| } | ||
| } | ||
| final int nBafs = beList.size(); | ||
| if ( nBafs == 1 ) { | ||
| writer.write(new BafEvidence(beList.get(0), .5)); | ||
| } else { | ||
| final RunningAverage ra = new RunningAverage(); | ||
| for ( final BafEvidence bafEvidence : beList ) { | ||
| ra.add(bafEvidence.getValue()); | ||
| } | ||
| final double stddev = ra.stddev(); | ||
| if ( stddev <= maxStdDev ) { | ||
| final double[] vals = new double[nBafs]; | ||
| for ( int idx = 0; idx != nBafs; ++idx ) { | ||
| vals[idx] = beList.get(idx).getValue(); | ||
| } | ||
| Arrays.sort(vals); | ||
| final int midIdx = nBafs / 2; | ||
| final double median = | ||
| (nBafs & 1) != 0 ? vals[midIdx] : (vals[midIdx] + vals[midIdx - 1])/2.; | ||
| final double adj = .5 - median; | ||
| for ( final BafEvidence bafEvidence : beList ) { | ||
| writer.write(new BafEvidence(bafEvidence, bafEvidence.getValue()+adj)); | ||
| } | ||
| } | ||
| } | ||
| sameLocusBuffer.clear(); | ||
| } | ||
|
|
||
| private VariantContext nextSite() { | ||
| while ( bafSitesIterator.hasNext() ) { | ||
| final VariantContext vc = bafSitesIterator.next(); | ||
| if ( vc.isSNP() && vc.isBiallelic() ) { | ||
| return vc; | ||
| } | ||
| } | ||
| throw new UserException("baf sites vcf exhausted before locus depth data"); | ||
| } | ||
| } |
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