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Adding docs

This commit is contained in:
Eric Banks 2011-08-17 13:27:36 -04:00
parent a21e193a9e
commit 6d629c176c
3 changed files with 48 additions and 14 deletions
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0
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java
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public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java
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public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
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@ -25,10 +25,8 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -43,21 +41,57 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import java.util.*;
/**
* Converts Sequenom files to a VCF annotated with QC metrics (HW-equilibrium, % failed probes)
* Annotates a validation (from e.g. Sequenom) VCF with QC metrics (HW-equilibrium, % failed probes)
*
* <p>
* The Variant Validation Assessor is a tool for vetting/assessing validation data (containing genotypes).
* The tool produces a VCF that is annotated with information pertaining to plate quality control and by
* default is soft-filtered by high no-call rate or low Hardy-Weinberg probability.
* If you have .ped files, please first convert them to VCF format
* (see http://www.broadinstitute.org/gsa/wiki/index.php/Converting_ped_to_vcf).
*
* <h2>Input</h2>
* <p>
* A validation VCF to annotate.
* </p>
*
* <h2>Output</h2>
* <p>
* An annotated VCF.
* </p>
*
* <h2>Examples</h2>
* <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T VariantValidationAssessor \
* --variant input.vcf \
* -o output.vcf
* </pre>
*
*/
@Reference(window=@Window(start=0,stop=40))
public class VariantValidationAssessor extends RodWalker<VariantContext,Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter vcfwriter = null;
@Argument(fullName="maxHardy", doc="Maximum phred-scaled Hardy-Weinberg violation pvalue to consider an assay valid [default:20]", required=false)
@Argument(fullName="maxHardy", doc="Maximum phred-scaled Hardy-Weinberg violation pvalue to consider an assay valid", required=false)
protected double maxHardy = 20.0;
@Argument(fullName="maxNoCall", doc="Maximum no-call rate (as a fraction) to consider an assay valid [default:0.05]", required=false)
/**
* To disable, set to a value greater than 1.
*/
@Argument(fullName="maxNoCall", doc="Maximum no-call rate (as a fraction) to consider an assay valid", required=false)
protected double maxNoCall = 0.05;
@Argument(fullName="maxHomVar", doc="Maximum homozygous variant rate (as a fraction) to consider an assay valid [default:1.1, disabled]", required=false)
/**
* To disable, set to a value greater than 1.
*/
@Argument(fullName="maxHomVar", doc="Maximum homozygous variant rate (as a fraction) to consider an assay valid", required=false)
protected double maxHomNonref = 1.1;
//@Argument(fullName="populationFile", shortName="populations", doc="A tab-delimited file relating individuals to populations,"+
@ -93,7 +127,7 @@ public class VariantValidationAssessor extends RodWalker<VariantContext,Integer>
if ( tracker == null )
return null;
VariantContext vc = tracker.getFirstValue(variants, ref.getLocus());
VariantContext vc = tracker.getFirstValue(variantCollection.variants, ref.getLocus());
// ignore places where we don't have a variant
if ( vc == null )
return null;
@ -101,7 +135,7 @@ public class VariantValidationAssessor extends RodWalker<VariantContext,Integer>
if ( sampleNames == null )
sampleNames = new TreeSet<String>(vc.getSampleNames());
return addVariantInformationToCall(ref, vc);
return addVariantInformationToCall(vc);
}
public Integer reduce(VariantContext call, Integer numVariants) {
@ -113,7 +147,7 @@ public class VariantValidationAssessor extends RodWalker<VariantContext,Integer>
}
public void onTraversalDone(Integer finalReduce) {
final List<String> inputNames = Arrays.asList(variants.getName());
final List<String> inputNames = Arrays.asList(variantCollection.variants.getName());
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
@ -159,7 +193,7 @@ public class VariantValidationAssessor extends RodWalker<VariantContext,Integer>
}
private VariantContext addVariantInformationToCall(ReferenceContext ref, VariantContext vContext) {
private VariantContext addVariantInformationToCall(VariantContext vContext) {
// check possible filters
double hwPvalue = hardyWeinbergCalculation(vContext);