LocusDepthtoBAF tool #7776
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change | ||||
|---|---|---|---|---|---|---|
| @@ -0,0 +1,270 @@ | ||||||
| package org.broadinstitute.hellbender.tools.sv; | ||||||
|
|
||||||
| 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; | ||||||
|
|
||||||
| import java.util.ArrayList; | ||||||
| import java.util.Arrays; | ||||||
| import java.util.Iterator; | ||||||
| import java.util.List; | ||||||
|
|
||||||
| /** | ||||||
| * <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 BIALLELIC_ONLY_NAME = "biallelic-only"; | ||||||
| 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; | ||||||
|
|
||||||
| @Argument(fullName = BAF_SITES_VCF_LONG_NAME, | ||||||
| doc = "Input VCF of SNPs marking loci for allele counts") | ||||||
| public GATKPath bafSitesFile; | ||||||
|
|
||||||
| @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; | ||||||
|
|
||||||
| @Argument( | ||||||
| doc = "Process only bi-allelic SNP sites", | ||||||
| fullName = BIALLELIC_ONLY_NAME, optional = true ) | ||||||
| private boolean biAllelicOnly = true; | ||||||
|
|
||||||
| @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; | ||||||
|
|
||||||
| @Argument( | ||||||
| doc = "Minimum probability of site being biallelic and heterozygous", | ||||||
| fullName = MIN_HET_PROBABILITY, optional = true ) | ||||||
| private double minHetProbability = .5; | ||||||
|
|
||||||
| @Argument( | ||||||
| doc = "Output compression level", | ||||||
| fullName = COMPRESSION_LEVEL_NAME, | ||||||
| minValue = 0, maxValue = 9, optional = true ) | ||||||
| private int compressionLevel = 4; | ||||||
|
|
||||||
| private FeatureDataSource<VariantContext> bafSitesSource; | ||||||
| private Iterator<VariantContext> bafSitesIterator; | ||||||
| private FeatureSink<BafEvidence> writer; | ||||||
| private final List<LocusDepth> sameLocusBuffer = new ArrayList<>(); | ||||||
|
|
||||||
| @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); | ||||||
| } | ||||||
|
|
||||||
| @Override | ||||||
| public void apply( LocusDepth locusDepth, Object header, | ||||||
| ReadsContext reads, ReferenceContext ref ) { | ||||||
| if ( !sameLocus(locusDepth) ) { | ||||||
| processBuffer(); | ||||||
| } | ||||||
| sameLocusBuffer.add(locusDepth); | ||||||
| } | ||||||
|
|
||||||
| @Override | ||||||
| public Object onTraversalSuccess() { | ||||||
| super.onTraversalSuccess(); | ||||||
| if ( !sameLocusBuffer.isEmpty() ) { | ||||||
| processBuffer(); | ||||||
| } | ||||||
| bafSitesSource.close(); | ||||||
| writer.close(); | ||||||
| return null; | ||||||
| } | ||||||
|
|
||||||
| /** 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; | ||||||
| } | ||||||
| double expectRefAlt = totalDepth / 2.; | ||||||
|
There was a problem hiding this comment.
Suggested change
|
||||||
| final double altDepth = locusDepth.getDepth(altIndex); | ||||||
| final double refDiff = locusDepth.getDepth(refIndex) - expectRefAlt; | ||||||
| final double altDiff = altDepth - expectRefAlt; | ||||||
| double chiSq = (refDiff * refDiff + altDiff * altDiff) / expectRefAlt; | ||||||
|
There was a problem hiding this comment.
Suggested change
|
||||||
| double fitProb = 1. - chiSqDist.cumulativeProbability(chiSq); | ||||||
|
There was a problem hiding this comment. Add comment that this is a Pearson chi-squared test There was a problem hiding this comment.
Suggested change
|
||||||
| if ( fitProb < minHetProbability ) { | ||||||
| return BafEvidence.MISSING_VALUE; | ||||||
| } | ||||||
| return altDepth / totalDepth; | ||||||
| } | ||||||
|
|
||||||
| 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(); | ||||||
| } | ||||||
|
|
||||||
| 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 nAlleles = alleles.size(); | ||||||
| final int[] altIndices = new int[nAlleles - 1]; | ||||||
| for ( int alleleIndex = 1; alleleIndex < nAlleles; ++alleleIndex ) { | ||||||
| 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()); | ||||||
| } | ||||||
| altIndices[alleleIndex - 1] = altIndex; | ||||||
| } | ||||||
| final List<BafEvidence> beList = new ArrayList<>(sameLocusBuffer.size()); | ||||||
| for ( final LocusDepth ld : sameLocusBuffer ) { | ||||||
| for ( final int altIndex : altIndices ) { | ||||||
| double baf = calcBAF(ld, refIndex, altIndex); | ||||||
| if ( baf != BafEvidence.MISSING_VALUE ) { | ||||||
| beList.add(new BafEvidence(ld.getSample(), ld.getContig(), ld.getStart(), baf)); | ||||||
| break; | ||||||
| } | ||||||
| } | ||||||
|
There was a problem hiding this comment. In some cases this will lead to bias. I didn't think through some of the problems multi-allelics are going to cause us with compatibility here. Apologies for flip-flopping on this, but let's stick to bi-allelic for both LD collection and BAF generation. Regardless, it seems like this implementation would be problematic in some edge cases. I think we will need to either provide the sites list to this tool, or go back to storing the ref/alt alleles in LD (which would be fine, probably simpler and faster). There was a problem hiding this comment. I'll remove the multi-allelic option, which kind of weirded me out anyway. There was a problem hiding this comment. Sorry just realized I missed that, all good to just rip out the multi-allelics. |
||||||
| } | ||||||
| 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); | ||||||
| int midIdx = nBafs / 2; | ||||||
| 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() && (!biAllelicOnly || vc.isBiallelic()) ) { | ||||||
| return vc; | ||||||
| } | ||||||
| } | ||||||
| throw new UserException("baf sites vcf exhausted before locus depth data"); | ||||||
| } | ||||||
| } | ||||||
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Can you please add a quick unit test for this?