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package org.broadinstitute.gatk.tools.walkers.validation;
import htsjdk.variant.vcf.*;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.walkers.*;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider;
import org.broadinstitute.gatk.utils.commandline.*;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.genotyper.*;
import org.broadinstitute.gatk.utils.SampleUtils;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import java.util.Map;
import java.util.Set;
import static org.broadinstitute.gatk.utils.IndelUtils.isInsideExtendedIndel;
/**
* Genotypes a dataset and validates the calls of another dataset using the Unified Genotyper.
*
* <h4>Note that this is an old tool that makes use of the UnifiedGenotyper, which has since been
* deprecated in favor of the HaplotypeCaller.</h4>
* <p>
* Genotype and Validate is a tool to evaluate the quality of a dataset for calling SNPs
* and Indels given a secondary (validation) data source. The data sources are BAM or VCF
* files. You can use them interchangeably (i.e. a BAM to validate calls in a VCF or a VCF
* to validate calls on a BAM).
* </p>
*
* <p>
* The simplest scenario is when you have a VCF of hand annotated SNPs and Indels, and you
* want to know how well a particular technology performs calling these snps. With a
* dataset (BAM file) generated by the technology in test, and the hand annotated VCF, you
* can run GenotypeAndValidate to asses the accuracy of the calls with the new technology's
* dataset.
* </p>
*
* <p>
* Another option is to validate the calls on a VCF file, using a deep coverage BAM file
* that you trust the calls on. The GenotypeAndValidate walker will make calls using the
* reads in the BAM file and take them as truth, then compare to the calls in the VCF file
* and produce a truth table.
* </p>
*
*
* <h3>Input</h3>
* <p>
* A BAM file to make calls on and a VCF file to use as truth validation dataset.
*
* You also have the option to invert the roles of the files using the command line options listed below.
* </p>
*
* <h3>Output</h3>
* <p>
* GenotypeAndValidate has two outputs. The truth table and the optional VCF file. The truth table is a
* 2x2 table correlating what was called in the dataset with the truth of the call (whether it's a true
* positive or a false positive). The table should look like this:
* </p>
* <center>
* <table id="description-table">
* <tr>
* <th></th>
* <th>ALT</th>
* <th>REF</th>
* <th>Predictive Value</th>
* </tr>
* <tr>
* <td><b>called alt</b></td>
* <td>True Positive (TP)</td>
* <td>False Positive (FP)</td>
* <td>Positive PV</td>
* </tr>
* <tr>
* <td><b>called ref</b></td>
* <td>False Negative (FN)</td>
* <td>True Negative (TN)</td>
* <td>Negative PV</td>
* </tr>
* </table>
* </center>
*
* <p>
* The <b>positive predictive value (PPV)</b> is the proportion of subjects with positive test results
* who are correctly diagnosed.
* </p>
* <p>
* The <b>negative predictive value (NPV)</b> is the proportion of subjects with a negative test result
* who are correctly diagnosed.
* </p>
* <p>
* The VCF file will contain only the variants that were called or not called, excluding the ones that
* were uncovered or didn't pass the filters. This file is useful if you are trying to compare
* the PPV and NPV of two different technologies on the exact same sites (so you can compare apples to
* apples).
* </p>
*
* <p>
* Here is an example of an annotated VCF file (info field clipped for clarity)
*
* <pre>
* #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
* 1 20568807 . C T 0 HapMapHet AC=1;AF=0.50;AN=2;DP=0;GV=T GT 0/1
* 1 22359922 . T C 282 WG-CG-HiSeq AC=2;AF=0.50;GV=T;AN=4;DP=42 GT:AD:DP:GL:GQ 1/0 ./. 0/1:20,22:39:-72.79,-11.75,-67.94:99 ./.
* 13 102391461 . G A 341 Indel;SnpCluster AC=1;GV=F;AF=0.50;AN=2;DP=45 GT:AD:DP:GL:GQ ./. ./. 0/1:32,13:45:-50.99,-13.56,-112.17:99 ./.
* 1 175516757 . C G 655 SnpCluster,WG AC=1;AF=0.50;AN=2;GV=F;DP=74 GT:AD:DP:GL:GQ ./. ./. 0/1:52,22:67:-89.02,-20.20,-191.27:99 ./.
* </pre>
*
* </p>
*
* <h3>Additional Details</h3>
* <ul>
* <li>
* You should always use -L on your VCF track, so that the GATK only looks at the sites on the VCF file.
* This speeds up the process a lot.
* </li>
* <li>
* The total number of visited bases may be greater than the number of variants in the original
* VCF file because of extended indels, as they trigger one call per new insertion or deletion.
* (i.e. ACTG/- will count as 4 genotyper calls, but it's only one line in the VCF).
* </li>
* </ul>
*
* <h3>Examples</h3>
* <ol>
* <li>
* Genotypes BAM file from new technology using the VCF as a truth dataset:
* </li>
*
* <pre>
* java
* -jar /GenomeAnalysisTK.jar
* -T GenotypeAndValidate
* -R human_g1k_v37.fasta
* -I myNewTechReads.bam
* -alleles handAnnotatedVCF.vcf
* -L handAnnotatedVCF.vcf
* </pre>
*
* <li>
* Using a BAM file as the truth dataset:
* </li>
*
* <pre>
* java
* -jar /GenomeAnalysisTK.jar
* -T GenotypeAndValidate
* -R human_g1k_v37.fasta
* -I myTruthDataset.bam
* -alleles callsToValidate.vcf
* -L callsToValidate.vcf
* -bt
* -o gav.vcf
* </pre>
*
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VALIDATION, extraDocs = {CommandLineGATK.class} )
@Requires(value={DataSource.READS, DataSource.REFERENCE})
@Allows(value={DataSource.READS, DataSource.REFERENCE})
@By(DataSource.REFERENCE)
@Reference(window=@Window(start=-200,stop=200))
public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedData, GenotypeAndValidate.CountedData> implements TreeReducible<GenotypeAndValidate.CountedData> {
/**
* The optional output file that will have all the variants used in the Genotype and Validation essay.
* The new annotation `callStatus` will carry the value called in the validation VCF or BAM file."
*/
@Output(doc="Output VCF file with annotated variants", required=false)
protected VariantContextWriter vcfWriter = null;
/**
* The callset to be used as truth (default) or validated (if BAM file is set to truth).
*/
@Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype", required=true)
public RodBinding<VariantContext> alleles;
/**
* Makes the Unified Genotyper calls to the BAM file the truth dataset and validates the alleles ROD binding callset.
*/
@Argument(fullName ="set_bam_truth", shortName ="bt", doc="Use the calls on the reads (bam file) as the truth dataset and validate the calls on the VCF", required=false)
private boolean bamIsTruth = false;
/**
* The minimum base quality score necessary for a base to be considered when calling a genotype. This argument is passed to the Unified Genotyper.
*/
@Argument(fullName="minimum_base_quality_score", shortName="mbq", doc="Minimum base quality score for calling a genotype", required=false)
private int mbq = -1;
/**
* The maximum deletion fraction allowed in a site for calling a genotype. This argument is passed to the Unified Genotyper.
*/
@Argument(fullName="maximum_deletion_fraction", shortName="deletions", doc="Maximum deletion fraction for calling a genotype", required=false)
private double deletions = -1;
/**
* the minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. This argument is passed to the Unified Genotyper.
*/
@Argument(fullName="standard_min_confidence_threshold_for_calling", shortName="stand_call_conf", doc="the minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls", required=false)
private double callConf = -1;
/**
* the minimum phred-scaled Qscore threshold to emit low confidence calls. This argument is passed to the Unified Genotyper.
*/
@Argument(fullName="standard_min_confidence_threshold_for_emitting", shortName="stand_emit_conf", doc="the minimum phred-scaled Qscore threshold to emit low confidence calls", required=false)
private double emitConf = -1;
/**
* Only validate sites that have at least a given depth
*/
@Argument(fullName="condition_on_depth", shortName="depth", doc="Condition validation on a minimum depth of coverage by the reads", required=false)
private int minDepth = -1;
/**
* Print out discordance sites to standard out.
*/
@Hidden
@Argument(fullName ="print_interesting_sites", shortName ="print_interesting", doc="Print out interesting sites to standard out", required=false)
private boolean printInterestingSites = false;
private UnifiedGenotypingEngine snpEngine;
private UnifiedGenotypingEngine indelEngine;
private Set<String> samples;
private enum GVstatus {
T, F, NONE
}
public static class CountedData {
private long nAltCalledAlt = 0L;
private long nAltCalledRef = 0L;
private long nAltNotCalled = 0L;
private long nRefCalledAlt = 0L;
private long nRefCalledRef = 0L;
private long nRefNotCalled = 0L;
private long nNoStatusCalledAlt = 0L;
private long nNoStatusCalledRef = 0L;
private long nNoStatusNotCalled = 0L;
private long nNotConfidentCalls = 0L;
private long nUncovered = 0L;
/**
* Adds the values of other to this, returning this
* @param other the other object
*/
public void add(CountedData other) {
nAltCalledAlt += other.nAltCalledAlt;
nAltCalledRef += other.nAltCalledRef;
nAltNotCalled += other.nAltNotCalled;
nRefCalledAlt += other.nRefCalledAlt;
nRefCalledRef += other.nRefCalledRef;
nRefNotCalled += other.nRefNotCalled;
nNoStatusCalledAlt += other.nNoStatusCalledAlt;
nNoStatusCalledRef += other.nNoStatusCalledRef;
nNoStatusNotCalled += other.nNoStatusNotCalled;
nUncovered += other.nUncovered;
nNotConfidentCalls += other.nNotConfidentCalls;
}
}
//---------------------------------------------------------------------------------------------------------------
//
// initialize
//
//---------------------------------------------------------------------------------------------------------------
public void initialize() {
// Initialize VCF header
if (vcfWriter != null) {
Map<String, VCFHeader> header = GATKVCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), alleles.getName());
samples = SampleUtils.getSampleList(header, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(header.values(), true);
headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate"));
headerLines.add(new VCFInfoHeaderLine("callStatus", 1, VCFHeaderLineType.String, "Value from the validation VCF"));
vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
}
// Filling in SNP calling arguments for UG
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
uac.outputMode = OutputMode.EMIT_ALL_SITES;
uac.alleles = alleles;
// TODO -- if we change this tool to actually validate against the called allele, then this if statement is needed;
// TODO -- for now, though, we need to be able to validate the right allele (because we only test isVariant below) [EB]
//if (!bamIsTruth)
uac.genotypingOutputMode = GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES;
if (mbq >= 0) uac.MIN_BASE_QUALTY_SCORE = mbq;
if (deletions >= 0)
uac.MAX_DELETION_FRACTION = deletions;
else
uac.MAX_DELETION_FRACTION = 1.0;
if (emitConf >= 0) uac.genotypeArgs.STANDARD_CONFIDENCE_FOR_EMITTING = emitConf;
if (callConf >= 0) uac.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING = callConf;
final GenomeAnalysisEngine toolkit = getToolkit();
uac.GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP;
snpEngine = new UnifiedGenotypingEngine(uac,
FixedAFCalculatorProvider.createThreadSafeProvider(toolkit, uac, logger),toolkit);
// Adding the INDEL calling arguments for UG
UnifiedArgumentCollection uac_indel = uac.clone();
uac_indel.GLmodel = GenotypeLikelihoodsCalculationModel.Model.INDEL;
indelEngine = new UnifiedGenotypingEngine(uac_indel,
FixedAFCalculatorProvider.createThreadSafeProvider(toolkit, uac, logger),toolkit);
// make sure we have callConf set to the threshold set by the UAC so we can use it later.
callConf = uac.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING;
}
//---------------------------------------------------------------------------------------------------------------
//
// map
//
//---------------------------------------------------------------------------------------------------------------
public CountedData map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
final CountedData counter = new CountedData();
// For some reason RodWalkers get map calls with null trackers
if( tracker == null )
return counter;
VariantContext vcComp = tracker.getFirstValue(alleles);
if( vcComp == null )
return counter;
//todo - not sure I want this, may be misleading to filter extended indel events.
if (isInsideExtendedIndel(vcComp, ref))
return counter;
// Do not operate on variants that are not covered to the optional minimum depth
if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
counter.nUncovered = 1L;
final GVstatus status = getGVstatus(vcComp);
if ( status == GVstatus.T )
counter.nAltNotCalled = 1L;
else if ( status == GVstatus.F )
counter.nRefNotCalled = 1L;
else
counter.nNoStatusNotCalled = 1L;
return counter;
}
VariantCallContext call;
if ( vcComp.isSNP() ) {
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0);
} else if ( vcComp.isIndel() ) {
call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0);
} else if ( bamIsTruth ) {
// assume it's a SNP if no variation is present; this is necessary so that we can test supposed monomorphic sites against the truth bam
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0);
} else {
logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
return counter;
}
boolean writeVariant = true;
if (bamIsTruth) {
if (call.confidentlyCalled) {
// If truth is a confident REF call
if (call.isVariant()) {
if (vcComp.isVariant())
counter.nAltCalledAlt = 1L;
else {
counter.nAltCalledRef = 1L;
if ( printInterestingSites )
System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart());
}
}
// If truth is a confident ALT call
else {
if (vcComp.isVariant()) {
counter.nRefCalledAlt = 1L;
if ( printInterestingSites )
System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart());
} else
counter.nRefCalledRef = 1L;
}
}
else {
counter.nNotConfidentCalls = 1L;
if ( printInterestingSites )
System.out.println("Truth is not confident at " + call.getChr() + ":" + call.getStart());
writeVariant = false;
}
}
else {
// if (!vcComp.hasExtendedAttribute("GV"))
// throw new UserException.BadInput("Variant has no GV annotation in the INFO field. " + vcComp.getChr() + ":" + vcComp.getStart());
final GVstatus status = getGVstatus(vcComp);
if (call.isCalledAlt(callConf)) {
if ( status == GVstatus.T )
counter.nAltCalledAlt = 1L;
else if ( status == GVstatus.F ) {
counter.nRefCalledAlt = 1L;
if ( printInterestingSites )
System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart());
}
else
counter.nNoStatusCalledAlt = 1L;
}
else if (call.isCalledRef(callConf)) {
if ( status == GVstatus.T ) {
counter.nAltCalledRef = 1L;
if ( printInterestingSites )
System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart());
}
else if ( status == GVstatus.F )
counter.nRefCalledRef = 1L;
else
counter.nNoStatusCalledRef = 1L;
}
else {
counter.nNotConfidentCalls = 1L;
if ( status == GVstatus.T )
counter.nAltNotCalled = 1L;
else if ( status == GVstatus.F )
counter.nRefNotCalled = 1L;
else
counter.nNoStatusNotCalled = 1L;
if ( printInterestingSites )
System.out.println("Truth is not confident at " + call.getChr() + ":" + call.getStart());
writeVariant = false;
}
}
if (vcfWriter != null && writeVariant) {
if (!vcComp.hasAttribute("callStatus")) {
vcfWriter.add(new VariantContextBuilder(vcComp).attribute("callStatus", call.isCalledAlt(callConf) ? "ALT" : "REF").make());
}
else
vcfWriter.add(vcComp);
}
return counter;
}
private GVstatus getGVstatus(final VariantContext vc) {
return ( !vc.hasAttribute("GV") ) ? GVstatus.NONE : (vc.getAttribute("GV").equals("T") ? GVstatus.T : GVstatus.F);
}
//---------------------------------------------------------------------------------------------------------------
//
// reduce
//
//---------------------------------------------------------------------------------------------------------------
public CountedData reduceInit() {
return new CountedData();
}
public CountedData treeReduce( final CountedData sum1, final CountedData sum2) {
sum2.add(sum1);
return sum2;
}
public CountedData reduce( final CountedData mapValue, final CountedData reduceSum ) {
reduceSum.add(mapValue);
return reduceSum;
}
public void onTraversalDone( CountedData reduceSum ) {
double ppv = 100 * ((double) reduceSum.nAltCalledAlt /( reduceSum.nAltCalledAlt + reduceSum.nRefCalledAlt));
double npv = 100 * ((double) reduceSum.nRefCalledRef /( reduceSum.nRefCalledRef + reduceSum.nAltCalledRef));
double sensitivity = 100 * ((double) reduceSum.nAltCalledAlt /( reduceSum.nAltCalledAlt + reduceSum.nAltCalledRef));
double specificity = (reduceSum.nRefCalledRef + reduceSum.nRefCalledAlt > 0) ? 100 * ((double) reduceSum.nRefCalledRef /( reduceSum.nRefCalledRef + reduceSum.nRefCalledAlt)) : 100;
logger.info(String.format("Resulting Truth Table Output\n\n" +
"------------------------------------------------------------------\n" +
"\t\t|\tALT\t|\tREF\t|\tNo Status\n" +
"------------------------------------------------------------------\n" +
"called alt\t|\t%d\t|\t%d\t|\t%d\n" +
"called ref\t|\t%d\t|\t%d\t|\t%d\n" +
"not called\t|\t%d\t|\t%d\t|\t%d\n" +
"------------------------------------------------------------------\n" +
"positive predictive value: %f%%\n" +
"negative predictive value: %f%%\n" +
"------------------------------------------------------------------\n" +
"sensitivity: %f%%\n" +
"specificity: %f%%\n" +
"------------------------------------------------------------------\n" +
"not confident: %d\n" +
"not covered: %d\n" +
"------------------------------------------------------------------\n", reduceSum.nAltCalledAlt, reduceSum.nRefCalledAlt, reduceSum.nNoStatusCalledAlt, reduceSum.nAltCalledRef, reduceSum.nRefCalledRef, reduceSum.nNoStatusCalledRef, reduceSum.nAltNotCalled, reduceSum.nRefNotCalled, reduceSum.nNoStatusNotCalled, ppv, npv, sensitivity, specificity, reduceSum.nNotConfidentCalls, reduceSum.nUncovered));
}
}