Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
This commit is contained in:
Eric Banks
commit
59945a41e8
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@ -92,7 +92,10 @@ public final class IntervalBinding<T extends Feature> {
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codec.readHeader(lineReader);
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String line = lineReader.readLine();
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while ( line != null ) {
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intervals.add(toolkit.getGenomeLocParser().createGenomeLoc(codec.decodeLoc(line)));
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final Feature feature = codec.decodeLoc(line);
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if ( feature == null )
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throw new UserException.MalformedFile(featureIntervals.getSource(), "Couldn't parse line '" + line + "'");
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intervals.add(toolkit.getGenomeLocParser().createGenomeLoc(feature));
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line = lineReader.readLine();
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}
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} catch (IOException e) {
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|
|
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@ -129,8 +129,14 @@ public class MalformedReadFilter extends ReadFilter {
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* @return true if they have the same number. False otherwise.
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*/
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private static boolean checkMismatchingBasesAndQuals(SAMRecord read, boolean filterMismatchingBaseAndQuals) {
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if (!filterMismatchingBaseAndQuals)
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throw new UserException.MalformedBAM(read, "BAM file has a read with mismatching number of bases and base qualities. Offender: " + read.getReadName() +" [" + read.getReadLength() + " bases] [" +read.getBaseQualities().length +"] quals");
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return (read.getReadLength() == read.getBaseQualities().length);
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boolean result;
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if (read.getReadLength() == read.getBaseQualities().length)
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result = true;
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else if (filterMismatchingBaseAndQuals)
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result = false;
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else
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throw new UserException.MalformedBAM(read, String.format("BAM file has a read with mismatching number of bases and base qualities. Offender: %s [%d bases] [%d quals]", read.getReadName(), read.getReadLength(), read.getBaseQualities().length));
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return result;
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}
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}
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@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval;
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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import net.sf.samtools.SAMSequenceRecord;
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import org.apache.log4j.Logger;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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@ -15,11 +16,14 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.gatk.walkers.TreeReducible;
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import org.broadinstitute.sting.gatk.walkers.Window;
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import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
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import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.IntervalStratification;
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import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.JexlExpression;
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import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
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import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche;
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import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
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@ -143,10 +147,10 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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/**
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* See the -list argument to view available modules.
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*/
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@Argument(fullName="evalModule", shortName="EV", doc="One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified)", required=false)
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@Argument(fullName="evalModule", shortName="EV", doc="One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noEV is specified)", required=false)
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protected String[] MODULES_TO_USE = {};
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@Argument(fullName="doNotUseAllStandardModules", shortName="noEV", doc="Do not use the standard modules by default (instead, only those that are specified with the -E option)", required=false)
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@Argument(fullName="doNotUseAllStandardModules", shortName="noEV", doc="Do not use the standard modules by default (instead, only those that are specified with the -EV option)", required=false)
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protected Boolean NO_STANDARD_MODULES = false;
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// Other arguments
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@ -171,6 +175,19 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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@Argument(fullName="requireStrictAlleleMatch", shortName="strict", doc="If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping", required=false)
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||||
private boolean requireStrictAlleleMatch = false;
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||||
|
||||
/**
|
||||
* If true, VariantEval will treat -eval 1 -eval 2 as separate tracks from the same underlying
|
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* variant set, and evaluate the union of the results. Useful when you want to do -eval chr1.vcf -eval chr2.vcf etc.
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*/
|
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@Argument(fullName="mergeEvals", shortName="mergeEvals", doc="If provided, all -eval tracks will be merged into a single eval track", required=false)
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public boolean mergeEvals = false;
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/**
|
||||
* File containing tribble-readable features for the IntervalStratificiation
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||||
*/
|
||||
@Input(fullName="stratIntervals", shortName="stratIntervals", doc="File containing tribble-readable features for the IntervalStratificiation", required=false)
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||||
protected IntervalBinding<Feature> intervalsFile = null;
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||||
|
||||
// Variables
|
||||
private Set<SortableJexlVCMatchExp> jexlExpressions = new TreeSet<SortableJexlVCMatchExp>();
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||||
|
||||
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@ -224,13 +241,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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knowns.add(compRod);
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}
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||||
|
||||
// Collect the eval rod names
|
||||
Set<String> evalNames = new TreeSet<String>();
|
||||
for ( RodBinding<VariantContext> evalRod : evals )
|
||||
evalNames.add(evalRod.getName());
|
||||
|
||||
// Now that we have all the rods categorized, determine the sample list from the eval rods.
|
||||
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), evalNames);
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Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), evals);
|
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Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
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// Load the sample list
|
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@ -258,6 +270,16 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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|||
perSampleIsEnabled = true;
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||||
}
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||||
|
||||
if ( intervalsFile != null ) {
|
||||
boolean fail = true;
|
||||
for ( final VariantStratifier vs : stratificationObjects ) {
|
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if ( vs.getClass().equals(IntervalStratification.class) )
|
||||
fail = false;
|
||||
}
|
||||
if ( fail )
|
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throw new UserException.BadArgumentValue("ST", "stratIntervals argument provided but -ST IntervalStratification not provided");
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||||
}
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// Initialize the evaluation contexts
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||||
evaluationContexts = variantEvalUtils.initializeEvaluationContexts(stratificationObjects, evaluationObjects, null, null);
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@ -289,8 +311,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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String aastr = (ancestralAlignments == null) ? null : new String(ancestralAlignments.getSubsequenceAt(ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStop()).getBases());
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||||
|
||||
// --------- track --------- sample - VariantContexts -
|
||||
HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled);
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HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false);
|
||||
HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled, mergeEvals);
|
||||
HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false, false);
|
||||
|
||||
// for each eval track
|
||||
for ( final RodBinding<VariantContext> evalRod : evals ) {
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||||
|
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@ -353,6 +375,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
|
|||
}
|
||||
}
|
||||
}
|
||||
|
||||
if ( mergeEvals ) break; // stop processing the eval tracks
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -528,6 +552,14 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
|
|||
|
||||
public Set<SortableJexlVCMatchExp> getJexlExpressions() { return jexlExpressions; }
|
||||
|
||||
public List<GenomeLoc> getIntervals() {
|
||||
if ( intervalsFile == null )
|
||||
throw new UserException.MissingArgument("stratIntervals", "Must be provided when IntervalStratification is enabled");
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||||
|
||||
return intervalsFile.getIntervals(getToolkit());
|
||||
}
|
||||
|
||||
|
||||
public Set<String> getContigNames() {
|
||||
final TreeSet<String> contigs = new TreeSet<String>();
|
||||
for( final SAMSequenceRecord r : getToolkit().getReferenceDataSource().getReference().getSequenceDictionary().getSequences()) {
|
||||
|
|
@ -536,4 +568,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
|
|||
return contigs;
|
||||
}
|
||||
|
||||
public GenomeLocParser getGenomeLocParser() {
|
||||
return getToolkit().getGenomeLocParser();
|
||||
}
|
||||
}
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||||
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@ -41,6 +41,9 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
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public long nDeletions = 0;
|
||||
@DataPoint(description = "Number of complex indels")
|
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public long nComplex = 0;
|
||||
@DataPoint(description = "Number of symbolic events")
|
||||
public long nSymbolic = 0;
|
||||
|
||||
@DataPoint(description = "Number of mixed loci (loci that can't be classified as a SNP, Indel or MNP)")
|
||||
public long nMixed = 0;
|
||||
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||||
|
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@ -131,8 +134,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
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nMixed++;
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break;
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case SYMBOLIC:
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||||
// ignore symbolic alleles, but don't fail
|
||||
// todo - consistent way of treating symbolic alleles thgoughout codebase?
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nSymbolic++;
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break;
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||||
default:
|
||||
throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
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||||
|
|
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|
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@ -0,0 +1,162 @@
|
|||
/*
|
||||
* Copyright (c) 2011, The Broad Institute
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
* OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
|
||||
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
|
||||
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
|
||||
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
import org.broadinstitute.sting.utils.variantcontext.Genotype;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.EnumMap;
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
@Analysis(description = "Build 1000 Genome Phase I paper summary of variants table")
|
||||
public class G1KPhaseITable extends VariantEvaluator {
|
||||
// basic counts on various rates found
|
||||
@DataPoint(description = "Number of samples")
|
||||
public long nSamples = 0;
|
||||
|
||||
@DataPoint(description = "Number of processed loci")
|
||||
public long nProcessedLoci = 0;
|
||||
|
||||
@DataPoint(description = "Number of SNPs")
|
||||
public long nSNPs = 0;
|
||||
@DataPoint(description = "SNP Novelty Rate")
|
||||
public double SNPNoveltyRate = 0;
|
||||
@DataPoint(description = "Mean number of SNPs per individual")
|
||||
public long nSNPsPerSample = 0;
|
||||
|
||||
@DataPoint(description = "Number of Indels")
|
||||
public long nIndels = 0;
|
||||
@DataPoint(description = "Indel Novelty Rate")
|
||||
public double IndelNoveltyRate = 0;
|
||||
@DataPoint(description = "Mean number of Indels per individual")
|
||||
public long nIndelsPerSample = 0;
|
||||
|
||||
@DataPoint(description = "Number of SVs")
|
||||
public long nSVs = 0;
|
||||
@DataPoint(description = "SV Novelty Rate")
|
||||
public double SVNoveltyRate = 0;
|
||||
@DataPoint(description = "Mean number of SVs per individual")
|
||||
public long nSVsPerSample = 0;
|
||||
|
||||
Map<VariantContext.Type, Integer> allVariantCounts, knownVariantCounts;
|
||||
Map<String, Map<VariantContext.Type, Integer>> countsPerSample;
|
||||
|
||||
private final Map<VariantContext.Type, Integer> makeCounts() {
|
||||
Map<VariantContext.Type, Integer> counts = new EnumMap<VariantContext.Type, Integer>(VariantContext.Type.class);
|
||||
counts.put(VariantContext.Type.SNP, 0);
|
||||
counts.put(VariantContext.Type.INDEL, 0);
|
||||
counts.put(VariantContext.Type.SYMBOLIC, 0);
|
||||
return counts;
|
||||
}
|
||||
|
||||
public void initialize(VariantEvalWalker walker) {
|
||||
countsPerSample = new HashMap<String, Map<VariantContext.Type, Integer>>();
|
||||
nSamples = walker.getSampleNamesForEvaluation().size();
|
||||
|
||||
for ( String sample : walker.getSampleNamesForEvaluation() ) {
|
||||
countsPerSample.put(sample, makeCounts());
|
||||
}
|
||||
|
||||
allVariantCounts = makeCounts();
|
||||
knownVariantCounts = makeCounts();
|
||||
}
|
||||
|
||||
@Override public boolean enabled() { return true; }
|
||||
|
||||
public int getComparisonOrder() {
|
||||
return 2; // we only need to see each eval track
|
||||
}
|
||||
|
||||
public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
nProcessedLoci += context.getSkippedBases() + (ref == null ? 0 : 1);
|
||||
}
|
||||
|
||||
public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
if ( eval == null || eval.isMonomorphic() ) return null;
|
||||
|
||||
switch (eval.getType()) {
|
||||
// case NO_VARIATION:
|
||||
// // shouldn't get here
|
||||
// break;
|
||||
case SNP:
|
||||
case INDEL:
|
||||
case SYMBOLIC:
|
||||
allVariantCounts.put(eval.getType(), allVariantCounts.get(eval.getType()) + 1);
|
||||
if ( comp != null )
|
||||
knownVariantCounts.put(eval.getType(), knownVariantCounts.get(eval.getType()) + 1);
|
||||
break;
|
||||
default:
|
||||
throw new UserException.BadInput("Unexpected variant context type: " + eval);
|
||||
}
|
||||
|
||||
// count variants per sample
|
||||
for (final Genotype g : eval.getGenotypes().values()) {
|
||||
if ( ! g.isNoCall() && ! g.isHomRef() ) {
|
||||
int count = countsPerSample.get(g.getSampleName()).get(eval.getType());
|
||||
countsPerSample.get(g.getSampleName()).put(eval.getType(), count + 1);
|
||||
}
|
||||
}
|
||||
|
||||
return null; // we don't capture any interesting sites
|
||||
}
|
||||
|
||||
private final int perSampleMean(VariantContext.Type type) {
|
||||
long sum = 0;
|
||||
for ( Map<VariantContext.Type, Integer> count : countsPerSample.values() ) {
|
||||
sum += count.get(type);
|
||||
}
|
||||
return (int)(Math.round(sum / (1.0 * countsPerSample.size())));
|
||||
}
|
||||
|
||||
private final double noveltyRate(VariantContext.Type type) {
|
||||
int all = allVariantCounts.get(type);
|
||||
int known = knownVariantCounts.get(type);
|
||||
int novel = all - known;
|
||||
return (novel / (1.0 * all));
|
||||
}
|
||||
|
||||
public void finalizeEvaluation() {
|
||||
nSNPs = allVariantCounts.get(VariantContext.Type.SNP);
|
||||
nIndels = allVariantCounts.get(VariantContext.Type.INDEL);
|
||||
nSVs = allVariantCounts.get(VariantContext.Type.SYMBOLIC);
|
||||
|
||||
nSNPsPerSample = perSampleMean(VariantContext.Type.SNP);
|
||||
nIndelsPerSample = perSampleMean(VariantContext.Type.INDEL);
|
||||
nSVsPerSample = perSampleMean(VariantContext.Type.SYMBOLIC);
|
||||
|
||||
SNPNoveltyRate = noveltyRate(VariantContext.Type.SNP);
|
||||
IndelNoveltyRate = noveltyRate(VariantContext.Type.INDEL);
|
||||
SVNoveltyRate = noveltyRate(VariantContext.Type.SYMBOLIC);
|
||||
}
|
||||
}
|
||||
|
|
@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
|||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
|
|
@ -15,8 +16,11 @@ public class EvalRod extends VariantStratifier implements RequiredStratification
|
|||
@Override
|
||||
public void initialize() {
|
||||
states = new ArrayList<String>();
|
||||
for ( RodBinding<VariantContext> rod : getVariantEvalWalker().getEvals() )
|
||||
for ( RodBinding<VariantContext> rod : getVariantEvalWalker().getEvals() ) {
|
||||
states.add(rod.getName());
|
||||
if ( getVariantEvalWalker().mergeEvals )
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
|
|
|
|||
|
|
@ -0,0 +1,93 @@
|
|||
/*
|
||||
* Copyright (c) 2011, The Broad Institute
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
* OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
|
||||
|
||||
import net.sf.picard.util.IntervalTree;
|
||||
import org.apache.log4j.Logger;
|
||||
import org.broad.tribble.Feature;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.GenomeLocParser;
|
||||
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
import org.broadinstitute.sting.utils.interval.IntervalUtils;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
/**
|
||||
* Stratifies the variants by whether they overlap an interval in the set provided on the command line.
|
||||
*
|
||||
* The primary use of this stratification is to provide a mechanism to divide asssessment of a call set up
|
||||
* by whether a variant overlaps an interval or not. I use this to differentiate between variants occurring
|
||||
* in CCDS exons vs. those in non-coding regions, in the 1000G call set, using a command line that looks like:
|
||||
*
|
||||
* -T VariantEval -R human_g1k_v37.fasta -eval 1000G.vcf -stratIntervals:BED ccds.bed -ST IntervalStratification
|
||||
*
|
||||
* Note that the overlap algorithm properly handles symbolic alleles with an INFO field END value. In order to
|
||||
* safely use this module you should provide entire contigs worth of variants, and let the interval strat decide
|
||||
* overlap, as opposed to using -L which will not properly work with symbolic variants.
|
||||
*/
|
||||
public class IntervalStratification extends VariantStratifier {
|
||||
final protected static Logger logger = Logger.getLogger(IntervalStratification.class);
|
||||
final Map<String, IntervalTree<Boolean>> intervalTreeByContig = new HashMap<String, IntervalTree<Boolean>>();
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
final List<GenomeLoc> locs = getVariantEvalWalker().getIntervals();
|
||||
|
||||
if ( locs.isEmpty() )
|
||||
throw new UserException.BadArgumentValue("stratIntervals", "Contains no intervals. Perhaps the file is malformed or empty?");
|
||||
|
||||
logger.info(String.format("Creating IntervalStratification containing %d intervals covering %d bp",
|
||||
locs.size(), IntervalUtils.intervalSize(locs)));
|
||||
|
||||
// set up the map from contig -> interval tree
|
||||
for ( final String contig : getVariantEvalWalker().getContigNames() )
|
||||
intervalTreeByContig.put(contig, new IntervalTree<Boolean>());
|
||||
|
||||
for ( final GenomeLoc loc : locs ) {
|
||||
intervalTreeByContig.get(loc.getContig()).put(loc.getStart(), loc.getStop(), true);
|
||||
}
|
||||
|
||||
states = new ArrayList<String>(Arrays.asList("all", "overlaps.intervals", "outside.intervals"));
|
||||
}
|
||||
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
final ArrayList<String> relevantStates = new ArrayList<String>(Arrays.asList("all"));
|
||||
|
||||
if (eval != null) {
|
||||
final GenomeLoc loc = getVariantEvalWalker().getGenomeLocParser().createGenomeLoc(eval, true);
|
||||
IntervalTree<Boolean> intervalTree = intervalTreeByContig.get(loc.getContig());
|
||||
IntervalTree.Node<Boolean> node = intervalTree.minOverlapper(loc.getStart(), loc.getStop());
|
||||
//logger.info(String.format("Overlap %s found %s", loc, node));
|
||||
relevantStates.add( node != null ? "overlaps.intervals" : "outside.intervals");
|
||||
}
|
||||
|
||||
return relevantStates;
|
||||
}
|
||||
}
|
||||
|
|
@ -312,12 +312,20 @@ public class VariantEvalUtils {
|
|||
*
|
||||
* @return the mapping of track to VC list that should be populated
|
||||
*/
|
||||
public HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, List<RodBinding<VariantContext>> tracks, boolean byFilter, boolean subsetBySample, boolean trackPerSample) {
|
||||
public HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>>
|
||||
bindVariantContexts(RefMetaDataTracker tracker,
|
||||
ReferenceContext ref,
|
||||
List<RodBinding<VariantContext>> tracks,
|
||||
boolean byFilter,
|
||||
boolean subsetBySample,
|
||||
boolean trackPerSample,
|
||||
boolean mergeTracks) {
|
||||
if ( tracker == null )
|
||||
return null;
|
||||
|
||||
HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> bindings = new HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>>();
|
||||
|
||||
RodBinding<VariantContext> firstTrack = tracks.isEmpty() ? null : tracks.get(0);
|
||||
for ( RodBinding<VariantContext> track : tracks ) {
|
||||
HashMap<String, Set<VariantContext>> mapping = new HashMap<String, Set<VariantContext>>();
|
||||
|
||||
|
|
@ -346,7 +354,20 @@ public class VariantEvalUtils {
|
|||
}
|
||||
}
|
||||
|
||||
bindings.put(track, mapping);
|
||||
if ( mergeTracks && bindings.containsKey(firstTrack) ) {
|
||||
// go through each binding of sample -> value and add all of the bindings from this entry
|
||||
HashMap<String, Set<VariantContext>> firstMapping = bindings.get(firstTrack);
|
||||
for ( Map.Entry<String, Set<VariantContext>> elt : mapping.entrySet() ) {
|
||||
Set<VariantContext> firstMappingSet = firstMapping.get(elt.getKey());
|
||||
if ( firstMappingSet != null ) {
|
||||
firstMappingSet.addAll(elt.getValue());
|
||||
} else {
|
||||
firstMapping.put(elt.getKey(), elt.getValue());
|
||||
}
|
||||
}
|
||||
} else {
|
||||
bindings.put(track, mapping);
|
||||
}
|
||||
}
|
||||
|
||||
return bindings;
|
||||
|
|
|
|||
|
|
@ -162,7 +162,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
|
|||
private boolean sitesOnlyVCF = false;
|
||||
|
||||
public void initialize() {
|
||||
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), null);
|
||||
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit());
|
||||
|
||||
if ( PRIORITY_STRING == null ) {
|
||||
PRIORITY_STRING = Utils.join(",", vcfRods.keySet());
|
||||
|
|
|
|||
|
|
@ -35,8 +35,10 @@ import net.sf.samtools.SAMSequenceDictionary;
|
|||
import net.sf.samtools.SAMSequenceRecord;
|
||||
import org.apache.log4j.Logger;
|
||||
import org.broad.tribble.Feature;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
/**
|
||||
* Factory class for creating GenomeLocs
|
||||
|
|
@ -453,6 +455,28 @@ public class GenomeLocParser {
|
|||
return createGenomeLoc(feature.getChr(), feature.getStart(), feature.getEnd());
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates a GenomeLoc corresponding to the variant context vc. If includeSymbolicEndIfPossible
|
||||
* is true, and VC is a symbolic allele the end of the created genome loc will be the value
|
||||
* of the END info field key, if it exists, or vc.getEnd() if not.
|
||||
*
|
||||
* @param vc
|
||||
* @param includeSymbolicEndIfPossible
|
||||
* @return
|
||||
*/
|
||||
public GenomeLoc createGenomeLoc(final VariantContext vc, boolean includeSymbolicEndIfPossible) {
|
||||
if ( includeSymbolicEndIfPossible && vc.isSymbolic() ) {
|
||||
int end = vc.getAttributeAsInt(VCFConstants.END_KEY, vc.getEnd());
|
||||
return createGenomeLoc(vc.getChr(), vc.getStart(), end);
|
||||
}
|
||||
else
|
||||
return createGenomeLoc(vc.getChr(), vc.getStart(), vc.getEnd());
|
||||
}
|
||||
|
||||
public GenomeLoc createGenomeLoc(final VariantContext vc) {
|
||||
return createGenomeLoc(vc, false);
|
||||
}
|
||||
|
||||
/**
|
||||
* create a new genome loc, given the contig name, and a single position. Must be on the reference
|
||||
*
|
||||
|
|
|
|||
|
|
@ -150,7 +150,7 @@ public class SampleUtils {
|
|||
|
||||
// iterate to get all of the sample names
|
||||
|
||||
for ( Map.Entry<String, VCFHeader> pair : VCFUtils.getVCFHeadersFromRods(toolkit, null).entrySet() ) {
|
||||
for ( Map.Entry<String, VCFHeader> pair : VCFUtils.getVCFHeadersFromRods(toolkit).entrySet() ) {
|
||||
Set<String> vcfSamples = pair.getValue().getGenotypeSamples();
|
||||
for ( String sample : vcfSamples )
|
||||
addUniqueSample(samples, sampleOverlapMap, rodNamesToSampleNames, sample, pair.getKey());
|
||||
|
|
|
|||
|
|
@ -26,6 +26,8 @@
|
|||
package org.broadinstitute.sting.utils.codecs.vcf;
|
||||
|
||||
import org.apache.log4j.Logger;
|
||||
import org.broad.tribble.Feature;
|
||||
import org.broadinstitute.sting.commandline.RodBinding;
|
||||
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
|
||||
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
|
@ -41,6 +43,18 @@ public class VCFUtils {
|
|||
*/
|
||||
private VCFUtils() { }
|
||||
|
||||
public static <T extends Feature> Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, List<RodBinding<T>> rodBindings) {
|
||||
// Collect the eval rod names
|
||||
final Set<String> names = new TreeSet<String>();
|
||||
for ( final RodBinding<T> evalRod : rodBindings )
|
||||
names.add(evalRod.getName());
|
||||
return getVCFHeadersFromRods(toolkit, names);
|
||||
}
|
||||
|
||||
public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit) {
|
||||
return getVCFHeadersFromRods(toolkit, (Collection<String>)null);
|
||||
}
|
||||
|
||||
public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
|
||||
Map<String, VCFHeader> data = new HashMap<String, VCFHeader>();
|
||||
|
||||
|
|
|
|||
|
|
@ -70,7 +70,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("1fefd6cf9c2554d5f886c3998defd4d0")
|
||||
Arrays.asList("fb926edfd3d811e18b33798a43ef4379")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
|
||||
}
|
||||
|
|
@ -91,7 +91,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("d470e00a368b5a0468012818994c6a89")
|
||||
Arrays.asList("26b7d57e3a204ac80a28cb29485b59b7")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
|
||||
}
|
||||
|
|
@ -113,7 +113,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("12856e52c2682328f91594089328596c")
|
||||
Arrays.asList("1df8184062f330bea9da8bacacc5a09d")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
|
||||
}
|
||||
|
|
@ -134,7 +134,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("91610b9240f64e0eb03cfd2602cf57af")
|
||||
Arrays.asList("927f26414509db9e7c0a2c067d57c949")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
|
||||
}
|
||||
|
|
@ -155,7 +155,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("e40b77e7ed6581328e373a24b93cd170")
|
||||
Arrays.asList("e6fddefd95122cabc5a0f0b95bce6d34")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
|
||||
}
|
||||
|
|
@ -176,7 +176,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("15beaf3823c131cabc5fb0445239f978")
|
||||
Arrays.asList("df10486dae73a9cf8c647964f51ba3e0")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
|
||||
}
|
||||
|
|
@ -197,7 +197,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("7ddd4ee74938d229ce5cb7b9b9104abe")
|
||||
Arrays.asList("524adb0b7ff70e227b8803a88f36713e")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
|
||||
}
|
||||
|
|
@ -220,7 +220,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("a90f33906a732ef5eb346e559c96ccc1")
|
||||
Arrays.asList("ef6449789dfc032602458b7c5538a1bc")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
|
||||
}
|
||||
|
|
@ -245,7 +245,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("2567f90d3d7354850c5a59730ecc6e4f")
|
||||
Arrays.asList("13b90e94fa82d72bb04a0a5addb27c3f")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
|
||||
}
|
||||
|
|
@ -264,7 +264,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("fa091aa8967893389c51102fd9f0bebb")
|
||||
Arrays.asList("8458b9d7803d75aae551fac7dbd152d6")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsNoCompRod", spec);
|
||||
}
|
||||
|
|
@ -277,7 +277,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
|
||||
" --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
|
||||
1, Arrays.asList("f70997b6a3e7fdc89d11e1d61a2463d4"));
|
||||
1, Arrays.asList("b954dee127ec4205ed7d33c91aa3e045"));
|
||||
executeTestParallel("testSelect1", spec);
|
||||
}
|
||||
|
||||
|
|
@ -294,7 +294,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testCompVsEvalAC() {
|
||||
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("407682de41dcf139ea635e9cda21b912"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ae0027197547731a9a5c1eec5fbe0221"));
|
||||
executeTestParallel("testCompVsEvalAC",spec);
|
||||
}
|
||||
|
||||
|
|
@ -324,7 +324,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --dbsnp " + b37dbSNP132 +
|
||||
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
|
||||
" -noST -ST Novelty -o %s";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("424c9d438b1faa59b2c29413ba32f37b"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("835b44fc3004cc975c968c9f92ed25d6"));
|
||||
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
|
||||
}
|
||||
|
||||
|
|
@ -336,7 +336,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
|
||||
" --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
|
||||
" -noST -ST Novelty -o %s";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("18fa0b89ebfff51141975d7e4ce7a159"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("f0e003f1293343c3210ae95e8936b19a"));
|
||||
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
|
||||
}
|
||||
|
||||
|
|
@ -414,8 +414,29 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("da65fc8f0d0eeaf0a0b06a07f444bb8e")
|
||||
Arrays.asList("924b6123edb9da540d0abc66f6f33e16")
|
||||
);
|
||||
executeTest("testAlleleCountStrat", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testIntervalStrat() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
buildCommandLine(
|
||||
"-T VariantEval",
|
||||
"-R " + b37KGReference,
|
||||
"-eval " + testDir + "/withSymbolic.b37.vcf",
|
||||
"-noEV",
|
||||
"-EV CountVariants",
|
||||
"-noST",
|
||||
"-stratIntervals " + testDir + "/overlapTest.bed",
|
||||
"-ST IntervalStratification",
|
||||
"-L 20",
|
||||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("9794e2dba205c6929dc89899fdf0bf6b")
|
||||
);
|
||||
executeTest("testIntervalStrat", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -129,9 +129,11 @@ class QCommandLine extends CommandLineProgram with Logging {
|
|||
logger.info("Writing JobLogging GATKReport to file " + reportFile)
|
||||
QJobReport.printReport(qGraph.getFunctionsAndStatus(script.functions), reportFile)
|
||||
|
||||
val pdfFile = new File(jobStringName + ".pdf")
|
||||
logger.info("Plotting JobLogging GATKReport to file " + pdfFile)
|
||||
QJobReport.plotReport(reportFile, pdfFile)
|
||||
if ( settings.run ) {
|
||||
val pdfFile = new File(jobStringName + ".pdf")
|
||||
logger.info("Plotting JobLogging GATKReport to file " + pdfFile)
|
||||
QJobReport.plotReport(reportFile, pdfFile)
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,3 @@
|
|||
20 315000 315100 # should overlap 2 in withSymbolic.vcf at 315006 and 315072
|
||||
20 316955 316959 # should overlap only deletion variant at 316952
|
||||
20 317900 400000 # should overlap only the symbolic variant at 317173
|
||||
|
|
@ -0,0 +1,96 @@
|
|||
##fileformat=VCFv4.1
|
||||
##INFO=<ID=LCSNP,Number=0,Type=Flag,Description="Genotype likelihood in Low coverage VCF in data integration">
|
||||
##INFO=<ID=EXSNP,Number=0,Type=Flag,Description="Genotype likelihood in Exome VCF in data integration">
|
||||
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Genotype likelihood in INDEL VCF in data integration">
|
||||
##INFO=<ID=SV,Number=0,Type=Flag,Description="Genotype likelihood in SV VCF in data integration">
|
||||
##INFO=<ID=BAVGPOST,Number=1,Type=Float,Description="Average posterior probability from beagle">
|
||||
##INFO=<ID=BRSQ,Number=1,Type=Float,Description="Genotype imputation quality estimate from beagle">
|
||||
##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
|
||||
##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
|
||||
##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
|
||||
##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
|
||||
##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
|
||||
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
|
||||
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
|
||||
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
|
||||
##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
|
||||
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
|
||||
##INFO=<ID=SOURCE,Number=.,Type=String,Description="Source of deletion call">
|
||||
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
|
||||
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
|
||||
##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
|
||||
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
|
||||
##ALT=<ID=DEL,Description="Deletion">
|
||||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
|
||||
##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
|
||||
##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
|
||||
##FORMAT=<ID=BD,Number=1,Type=Float,Description="Genotype dosage from beagle">
|
||||
#CHROM POS ID REF ALT QUAL FILTER INFO
|
||||
20 315006 . A G 100 PASS LCSNP;EXSNP;BAVGPOST=0.998;BRSQ=0.721;LDAF=0.0025;AVGPOST=0.9978;RSQ=0.6449;ERATE=0.0008;THETA=0.0006;AC=4;AN=2184
|
||||
20 315072 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.996;LDAF=0.0057;AVGPOST=0.9996;RSQ=0.9743;ERATE=0.0003;THETA=0.0016;AC=12;AN=2184
|
||||
20 315162 . T G 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.950;LDAF=0.0005;AVGPOST=0.9998;RSQ=0.8078;ERATE=0.0003;THETA=0.0004;AC=1;AN=2184
|
||||
20 315168 rs71327439 G GA 7142 PASS INDEL;BAVGPOST=0.999;BRSQ=0.990;LDAF=0.0575;AVGPOST=0.9985;RSQ=0.9891;ERATE=0.0003;THETA=0.0004;AC=125;AN=2184
|
||||
20 315201 . A G 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.965;LDAF=0.0005;AVGPOST=0.9999;RSQ=0.8599;ERATE=0.0003;THETA=0.0008;AC=1;AN=2184
|
||||
20 315214 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.974;LDAF=0.0009;AVGPOST=0.9990;RSQ=0.5860;ERATE=0.0003;THETA=0.0005;AC=1;AN=2184
|
||||
20 315270 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.999;LDAF=0.0557;AVGPOST=0.9992;RSQ=0.9950;ERATE=0.0003;THETA=0.0004;AC=121;AN=2184
|
||||
20 315279 . A G 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.991;LDAF=0.0572;AVGPOST=0.9990;RSQ=0.9926;ERATE=0.0003;THETA=0.0013;AC=125;AN=2184
|
||||
20 315320 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.995;LDAF=0.0028;AVGPOST=0.9998;RSQ=0.9594;ERATE=0.0005;THETA=0.0003;AC=6;AN=2184
|
||||
20 315322 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.814;LDAF=0.0007;AVGPOST=0.9994;RSQ=0.6510;ERATE=0.0003;THETA=0.0004;AC=1;AN=2184
|
||||
20 315431 . A T 100 PASS LCSNP;EXSNP;BAVGPOST=0.987;BRSQ=0.864;LDAF=0.0431;AVGPOST=0.9873;RSQ=0.8675;ERATE=0.0006;THETA=0.0010;AC=86;AN=2184
|
||||
20 315481 . T A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.998;LDAF=0.0619;AVGPOST=0.9993;RSQ=0.9948;ERATE=0.0003;THETA=0.0007;AC=135;AN=2184
|
||||
20 315490 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.984;LDAF=0.0138;AVGPOST=0.9971;RSQ=0.9260;ERATE=0.0003;THETA=0.0046;AC=31;AN=2184
|
||||
20 315523 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.822;LDAF=0.0015;AVGPOST=0.9988;RSQ=0.6777;ERATE=0.0005;THETA=0.0003;AC=2;AN=2184
|
||||
20 315547 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.893;LDAF=0.0026;AVGPOST=0.9995;RSQ=0.9024;ERATE=0.0003;THETA=0.0004;AC=5;AN=2184
|
||||
20 315549 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.888;LDAF=0.0029;AVGPOST=0.9988;RSQ=0.8565;ERATE=0.0003;THETA=0.0013;AC=5;AN=2184
|
||||
20 315551 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.829;LDAF=0.0008;AVGPOST=0.9992;RSQ=0.5723;ERATE=0.0003;THETA=0.0012;AC=1;AN=2184
|
||||
20 315704 . G C 100 PASS LCSNP;EXSNP;BAVGPOST=0.998;BRSQ=0.945;LDAF=0.0184;AVGPOST=0.9978;RSQ=0.9523;ERATE=0.0003;THETA=0.0017;AC=40;AN=2184
|
||||
20 315798 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.773;LDAF=0.0012;AVGPOST=0.9985;RSQ=0.4929;ERATE=0.0003;THETA=0.0005;AC=1;AN=2184
|
||||
20 315842 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.979;LDAF=0.0110;AVGPOST=0.9991;RSQ=0.9673;ERATE=0.0003;THETA=0.0005;AC=23;AN=2184
|
||||
20 315876 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.926;LDAF=0.0018;AVGPOST=0.9988;RSQ=0.7731;ERATE=0.0003;THETA=0.0007;AC=3;AN=2184
|
||||
20 316028 . G C 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.999;LDAF=0.0714;AVGPOST=0.9997;RSQ=0.9982;ERATE=0.0003;THETA=0.0003;AC=156;AN=2184
|
||||
20 316055 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.997;LDAF=0.1006;AVGPOST=0.9993;RSQ=0.9969;ERATE=0.0003;THETA=0.0007;AC=220;AN=2184
|
||||
20 316137 . G C 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.976;LDAF=0.0037;AVGPOST=0.9982;RSQ=0.7861;ERATE=0.0004;THETA=0.0009;AC=6;AN=2184
|
||||
20 316142 . C A 100 PASS LCSNP;EXSNP;BAVGPOST=0.998;BRSQ=0.793;LDAF=0.0033;AVGPOST=0.9980;RSQ=0.7527;ERATE=0.0003;THETA=0.0003;AC=6;AN=2184
|
||||
20 316143 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.839;LDAF=0.0034;AVGPOST=0.9984;RSQ=0.8054;ERATE=0.0003;THETA=0.0003;AC=6;AN=2184
|
||||
20 316211 . C G 100 PASS LCSNP;EXSNP;BAVGPOST=0.997;BRSQ=0.976;LDAF=0.0565;AVGPOST=0.9983;RSQ=0.9872;ERATE=0.0003;THETA=0.0010;AC=124;AN=2184
|
||||
20 316285 . A AT 5514 PASS INDEL;BAVGPOST=0.999;BRSQ=0.993;LDAF=0.0552;AVGPOST=0.9978;RSQ=0.9829;ERATE=0.0004;THETA=0.0005;AC=119;AN=2184
|
||||
20 316295 . A G 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.808;LDAF=0.0021;AVGPOST=0.9980;RSQ=0.6390;ERATE=0.0003;THETA=0.0008;AC=4;AN=2184
|
||||
20 316481 . G T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=1.000;LDAF=0.0499;AVGPOST=0.9997;RSQ=0.9970;ERATE=0.0003;THETA=0.0007;AC=109;AN=2184
|
||||
20 316488 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.897;LDAF=0.0011;AVGPOST=0.9997;RSQ=0.8509;ERATE=0.0003;THETA=0.0006;AC=2;AN=2184
|
||||
20 316553 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.945;LDAF=0.0007;AVGPOST=0.9996;RSQ=0.7074;ERATE=0.0003;THETA=0.0004;AC=1;AN=2184
|
||||
20 316659 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.998;LDAF=0.0497;AVGPOST=0.9995;RSQ=0.9960;ERATE=0.0003;THETA=0.0007;AC=109;AN=2184
|
||||
20 316691 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.985;LDAF=0.0058;AVGPOST=0.9989;RSQ=0.9301;ERATE=0.0003;THETA=0.0003;AC=13;AN=2184
|
||||
20 316700 . A G 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.737;LDAF=0.0030;AVGPOST=0.9971;RSQ=0.5700;ERATE=0.0009;THETA=0.0016;AC=4;AN=2184
|
||||
20 316725 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.853;LDAF=0.0011;AVGPOST=0.9995;RSQ=0.7944;ERATE=0.0003;THETA=0.0004;AC=2;AN=2184
|
||||
20 316770 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.966;LDAF=0.0017;AVGPOST=0.9991;RSQ=0.7543;ERATE=0.0005;THETA=0.0005;AC=3;AN=2184
|
||||
20 316813 . GTTC G 1701 PASS INDEL;BAVGPOST=0.995;BRSQ=0.850;LDAF=0.0156;AVGPOST=0.9987;RSQ=0.9611;ERATE=0.0003;THETA=0.0006;AC=34;AN=2184
|
||||
20 316824 rs11472305 T TTTC 5129 PASS INDEL;BAVGPOST=0.979;BRSQ=0.863;LDAF=0.0697;AVGPOST=0.9782;RSQ=0.8837;ERATE=0.0016;THETA=0.0006;AC=153;AN=2184
|
||||
20 316839 . CT C 1122 PASS INDEL;BAVGPOST=0.980;BRSQ=0.804;LDAF=0.0505;AVGPOST=0.9743;RSQ=0.8100;ERATE=0.0040;THETA=0.0009;AC=104;AN=2184
|
||||
20 316841 . TTC T 1096 PASS INDEL;BAVGPOST=0.981;BRSQ=0.824;LDAF=0.0491;AVGPOST=0.9783;RSQ=0.8367;ERATE=0.0029;THETA=0.0005;AC=105;AN=2184
|
||||
20 316842 . TCC T 110 PASS INDEL;BAVGPOST=0.983;BRSQ=0.592;LDAF=0.0203;AVGPOST=0.9772;RSQ=0.5576;ERATE=0.0022;THETA=0.0005;AC=30;AN=2184
|
||||
20 316845 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.645;LDAF=0.0015;AVGPOST=0.9989;RSQ=0.6666;ERATE=0.0003;THETA=0.0010;AC=2;AN=2184
|
||||
20 316853 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=0.990;BRSQ=0.922;LDAF=0.0688;AVGPOST=0.9742;RSQ=0.8456;ERATE=0.0049;THETA=0.0006;AC=133;AN=2184
|
||||
20 316882 rs11479165 CT C 145 PASS INDEL;BAVGPOST=0.991;BRSQ=0.484;LDAF=0.0074;AVGPOST=0.9920;RSQ=0.5655;ERATE=0.0005;THETA=0.0014;AC=9;AN=2184
|
||||
20 316889 . T TTC 108 PASS INDEL;BAVGPOST=0.978;BRSQ=0.235;LDAF=0.0521;AVGPOST=0.9304;RSQ=0.4479;ERATE=0.0035;THETA=0.0016;AC=63;AN=2184
|
||||
20 316901 . T TTC 272 PASS INDEL;BAVGPOST=0.979;BRSQ=0.510;LDAF=0.0363;AVGPOST=0.9527;RSQ=0.4348;ERATE=0.0071;THETA=0.0003;AC=34;AN=2184
|
||||
20 316917 . CT C 67 PASS INDEL;BAVGPOST=0.983;BRSQ=0.483;LDAF=0.0265;AVGPOST=0.9828;RSQ=0.7509;ERATE=0.0006;THETA=0.0011;AC=51;AN=2184
|
||||
20 316918 rs112071142 TTTC T 3049 PASS INDEL;BAVGPOST=0.980;BRSQ=0.801;LDAF=0.0588;AVGPOST=0.9761;RSQ=0.8444;ERATE=0.0026;THETA=0.0005;AC=120;AN=2184
|
||||
20 316924 . CT C 8 PASS INDEL;BAVGPOST=0.999;BRSQ=0.581;LDAF=0.0053;AVGPOST=0.9932;RSQ=0.5513;ERATE=0.0004;THETA=0.0011;AC=6;AN=2184
|
||||
20 316936 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=0.994;BRSQ=0.651;LDAF=0.0098;AVGPOST=0.9884;RSQ=0.5505;ERATE=0.0018;THETA=0.0005;AC=13;AN=2184
|
||||
20 316939 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=0.997;BRSQ=0.720;LDAF=0.0071;AVGPOST=0.9899;RSQ=0.4845;ERATE=0.0010;THETA=0.0033;AC=8;AN=2184
|
||||
20 316952 . CTCTTCCTCTTCT C 15835 PASS INDEL;BAVGPOST=0.891;BRSQ=0.667;LDAF=0.1650;AVGPOST=0.9042;RSQ=0.7274;ERATE=0.0037;THETA=0.0008;AC=294;AN=2184
|
||||
20 317003 . TCC T 333 PASS INDEL;BAVGPOST=0.890;BRSQ=0.114;LDAF=0.3450;AVGPOST=0.5526;RSQ=0.1674;ERATE=0.0300;THETA=0.0011;AC=350;AN=2184
|
||||
20 317022 rs111424933 TTTC T 4776 PASS INDEL;BAVGPOST=0.982;BRSQ=0.865;LDAF=0.0561;AVGPOST=0.9837;RSQ=0.8889;ERATE=0.0017;THETA=0.0004;AC=110;AN=2184
|
||||
20 317057 . C A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.775;LDAF=0.0014;AVGPOST=0.9985;RSQ=0.6049;ERATE=0.0003;THETA=0.0002;AC=3;AN=2184
|
||||
20 317135 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=0.995;BRSQ=0.992;LDAF=0.0489;AVGPOST=0.9964;RSQ=0.9749;ERATE=0.0004;THETA=0.0025;AC=106;AN=2184
|
||||
20 317173 MERGED_DEL_2_99440 A <DEL> . . SV;BAVGPOST=0.998;BRSQ=0.577;LDAF=0.0018;AVGPOST=0.9990;RSQ=0.7465;ERATE=0.0003;THETA=0.0007;CIEND=-61,92;CIPOS=-84,73;END=319201;SOURCE=BreakDancer_317182_319211,GenomeStrip_317164_319190;SVTYPE=DEL;AC=2;AN=2184
|
||||
20 317174 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=0.995;BRSQ=0.991;LDAF=0.0502;AVGPOST=0.9962;RSQ=0.9727;ERATE=0.0005;THETA=0.0007;AC=107;AN=2184
|
||||
20 317266 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.999;LDAF=0.1748;AVGPOST=0.9988;RSQ=0.9973;ERATE=0.0003;THETA=0.0005;AC=383;AN=2184
|
||||
20 317448 . A G 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.999;LDAF=0.0068;AVGPOST=0.9988;RSQ=0.9405;ERATE=0.0003;THETA=0.0002;AC=16;AN=2184
|
||||
20 317491 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.991;LDAF=0.0609;AVGPOST=0.9993;RSQ=0.9939;ERATE=0.0003;THETA=0.0004;AC=133;AN=2184
|
||||
20 317546 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.837;LDAF=0.0007;AVGPOST=0.9994;RSQ=0.6154;ERATE=0.0003;THETA=0.0012;AC=1;AN=2184
|
||||
20 317578 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=0.996;BRSQ=0.882;LDAF=0.0180;AVGPOST=0.9981;RSQ=0.9606;ERATE=0.0003;THETA=0.0004;AC=40;AN=2184
|
||||
20 317658 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=1.000;LDAF=0.0609;AVGPOST=0.9998;RSQ=0.9980;ERATE=0.0003;THETA=0.0005;AC=133;AN=2184
|
||||
20 317676 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=1.000;LDAF=0.0608;AVGPOST=0.9999;RSQ=0.9992;ERATE=0.0003;THETA=0.0004;AC=133;AN=2184
|
||||
20 317710 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.952;LDAF=0.0014;AVGPOST=0.9997;RSQ=0.8880;ERATE=0.0004;THETA=0.0008;AC=3;AN=2184
|
||||
20 317824 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.999;LDAF=0.0555;AVGPOST=0.9993;RSQ=0.9947;ERATE=0.0003;THETA=0.0009;AC=121;AN=2184
|
||||
Loading…
Reference in New Issue