GenotypeAndValidate: now looks at annotations in the INFO field instead of filter field. Better output and filters repetitive calls to indel extended events.
IndelUtils: added a isInsideExtendedIndel() method to filter the above mentioned. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5449 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro
parent
d98503ca50
commit
e2e435d52c
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@ -23,9 +23,8 @@
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.oneoffprojects.walkers;
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package org.broadinstitute.sting.playground.gatk.walkers;
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import com.google.common.collect.ImmutableSet;
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import org.broad.tribble.util.variantcontext.MutableVariantContext;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.VCFHeader;
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@ -46,10 +45,11 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.vcf.VCFUtils;
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import sun.management.counter.Variability;
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import java.util.*;
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import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
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/**
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* Validates the calls on a ROD track using a BAM dataset.
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*
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@ -77,6 +77,12 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
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@Argument(fullName="maximum_deletion_fraction", shortName="deletions", doc="Maximum deletion fraction for calling a genotype", required=false)
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private double deletions = -1;
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@Argument(fullName="standard_min_confidence_threshold_for_calling", shortName="stand_call_conf", doc="he minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls", required=false)
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private double callConf = -1;
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@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)
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private double emitConf = -1;
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@Argument(fullName="condition_on_depth", shortName="depth", doc="Condition validation on a minimum depth of coverage by the reads", required=false)
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private int minDepth = -1;
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@ -140,6 +146,10 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
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uac.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
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if (mbq >= 0) uac.MIN_BASE_QUALTY_SCORE = mbq;
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if (deletions >= 0) uac.MAX_DELETION_FRACTION = deletions;
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if (callConf >= 0) uac.STANDARD_CONFIDENCE_FOR_CALLING = callConf;
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if (emitConf >= 0) uac.STANDARD_CONFIDENCE_FOR_EMITTING = emitConf;
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snpEngine = new UnifiedGenotyperEngine(getToolkit(), uac);
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// Adding the INDEL calling arguments for UG
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@ -165,16 +175,18 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
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if( vcComp == null )
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return counter;
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//todo - not sure I want this, may be misleading to filter extended indel events.
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if (isInsideExtendedIndel(vcComp, ref))
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return counter;
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// Do not operate on variants that are not covered to the optional minimum depth
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if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
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// don't count indel extended events multiple times as uncovered.
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// if (vcComp.getStart() == ref.getLocus().getStart()) //todo - not sure I want this, may be misleading to filter anything.
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counter.numUncovered = 1L;
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counter.numUncovered = 1L;
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return counter;
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}
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if ((vcComp.getFilters().contains("TP") && vcComp.getFilters().contains("FP")) || (!vcComp.getFilters().contains("TP") && !vcComp.getFilters().contains("FP")))
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throw new UserException.BadInput("Variant has the wrong filter annotation -- either missing FP/TP or has both. " + vcComp.getChr() + ":" + vcComp.getStart());
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if (!vcComp.hasAttribute("GV"))
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throw new UserException.BadInput("Variant has no GV annotation in the INFO field. " + vcComp.getChr() + ":" + vcComp.getStart());
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VariantCallContext call;
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if ( vcComp.isSNP() )
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@ -189,16 +201,16 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
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return counter;
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}
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if (!call.confidentlyCalled) { //todo - maybe filter extended indel events to count as one only if it's entirely successful?
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if (!call.confidentlyCalled) {
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counter.numNotConfidentCalls = 1L;
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if (vcComp.getFilters().contains("TP"))
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if (vcComp.getAttribute("GV").equals("T"))
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counter.numFN = 1L;
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else
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counter.numTN = 1L;
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}
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else {
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counter.numConfidentCalls = 1L;
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if (vcComp.getFilters().contains("TP"))
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if (vcComp.getAttribute("GV").equals("T"))
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counter.numTP = 1L;
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else
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counter.numFP = 1L;
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@ -229,7 +241,23 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
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}
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public void onTraversalDone( CountedData reduceSum ) {
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logger.info("(status / truth)");
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double ppv = 100 * ((double) reduceSum.numTP /( reduceSum.numTP + reduceSum.numFP));
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double npv = 100 * ((double) reduceSum.numTN /( reduceSum.numTN + reduceSum.numFN));
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logger.info(String.format("Resulting Truth Table Output\n\n" +
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"---------------------------------------------------\n" +
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"\t\t|\tT\t|\tF\t\n" +
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"---------------------------------------------------\n" +
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"called alt\t|\t%d\t|\t%d\n" +
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"called ref\t|\t%d\t|\t%d\n" +
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"---------------------------------------------------\n" +
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"positive predictive value: %f%%\n" +
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"negative predictive value: %f%%\n" +
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"---------------------------------------------------\n" +
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"uncovered: %d\n" +
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"---------------------------------------------------\n", reduceSum.numTP, reduceSum.numFP, reduceSum.numFN, reduceSum.numTN, ppv, npv, reduceSum.numUncovered));
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/*
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logger.info("called / true = " + reduceSum.numTP);
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logger.info("not called / false = " + reduceSum.numTN);
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logger.info("called /false = " + reduceSum.numFP);
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@ -239,5 +267,6 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
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logger.info("confidently called = " + reduceSum.numConfidentCalls);
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logger.info("not confidently called = " + reduceSum.numNotConfidentCalls );
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logger.info("Uncovered = " + reduceSum.numUncovered);
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*/
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}
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}
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@ -264,4 +264,7 @@ public class IndelUtils {
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}
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public static boolean isInsideExtendedIndel(VariantContext vc, ReferenceContext ref) {
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return (vc.getStart() != ref.getLocus().getStart());
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}
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}
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