Fixed the QUAL calculation of the EXACT_INDEPENDENT.
The QUAL value calculated by this Exact AF Calculator is very underestimated when there are more than one alternative allele (non-biallelic sites). The reason is that the QUAL was roughly calculated by adding the QUALs resulting of each alternative alleles vs all other alleles, reference and alts, collapsed. This is ok for MLEAC calculations but not for QUAL. Now, for calculating the QUAL we collapse all the alternatives as only one. This change improves sensitivy with a cost of additional false positives, but this is naturally expected. The resulting QUAL column is much closer to the one returned by the reference implementation. Story: https://www.pivotaltracker.com/story/show/75926368. Changes: Changed the QUAL calculation as described above. Updated MD5s. Fixed MD5s
This commit is contained in:
Valentin Ruano-Rubio
parent
f7fc9cd839
commit
311b6815b3
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@ -48,8 +48,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
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import com.google.java.contract.Ensures;
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import com.google.java.contract.Requires;
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import org.broadinstitute.gatk.utils.MathUtils;
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import htsjdk.variant.variantcontext.*;
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import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators;
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import org.broadinstitute.gatk.utils.MathUtils;
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import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
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import java.util.*;
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@ -167,9 +169,54 @@ import java.util.*;
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// fast path for the very common bi-allelic use case
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return independentResultTrackers.get(0);
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} else {
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final AFCalculationResult combinedAltAllelesResult = combineAltAlleleIndependentExact(vc,defaultPloidy,log10AlleleFrequencyPriors);
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// we are a multi-allelic, so we need to actually combine the results
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final List<AFCalculationResult> withMultiAllelicPriors = applyMultiAllelicPriors(independentResultTrackers);
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return combineIndependentPNonRefs(vc, withMultiAllelicPriors);
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return combineIndependentPNonRefs(vc, withMultiAllelicPriors, combinedAltAllelesResult);
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}
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}
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private AFCalculationResult combineAltAlleleIndependentExact(final VariantContext vc, int defaultPloidy, double[] log10AlleleFrequencyPriors) {
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final VariantContext combinedAltAllelesVariantContext = makeCombinedAltAllelesVariantContext(vc);
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final AFCalculationResult resultTracker = biAlleleExactModel.getLog10PNonRef(combinedAltAllelesVariantContext, defaultPloidy, vc.getNAlleles() - 1, log10AlleleFrequencyPriors);
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return resultTracker;
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}
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private VariantContext makeCombinedAltAllelesVariantContext(final VariantContext vc) {
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final int nAltAlleles = vc.getNAlleles() - 1;
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if ( nAltAlleles == 1 )
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return vc;
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else {
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final VariantContextBuilder vcb = new VariantContextBuilder(vc);
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final Allele reference = vcb.getAlleles().get(0);
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vcb.alleles(Arrays.asList(reference, GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE));
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final int genotypeCount = GenotypeLikelihoodCalculators.genotypeCount(2, vc.getNAlleles());
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final double[] hetLikelihoods = new double[vc.getNAlleles() - 1];
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final double[] homAltLikelihoods = new double[genotypeCount - hetLikelihoods.length - 1];
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final double[] newLikelihoods = new double[3];
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final List<Genotype> newGenotypes = new ArrayList<>(vc.getNSamples());
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for (final Genotype oldGenotype : vc.getGenotypes()) {
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final GenotypeBuilder gb = new GenotypeBuilder(oldGenotype);
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final List<Allele> oldAlleles = oldGenotype.getAlleles();
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if (oldAlleles != null) {
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final List<Allele> newAlleles = new ArrayList<>(oldAlleles.size());
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for (int i = 0; i < oldAlleles.size(); i++) {
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final Allele oldAllele = oldAlleles.get(i);
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if (oldAllele.isReference())
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newAlleles.add(reference);
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else if (oldAllele.isNoCall())
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newAlleles.add(Allele.NO_CALL);
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else
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newAlleles.add(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
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}
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gb.alleles(newAlleles);
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}
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if (combineAltAlleleLikelihoods(oldGenotype, genotypeCount, newLikelihoods, hetLikelihoods, homAltLikelihoods))
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gb.PL(newLikelihoods);
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newGenotypes.add(gb.make());
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}
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return vcb.genotypes(newGenotypes).make();
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}
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}
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@ -427,18 +474,17 @@ import java.util.*;
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* @param sortedResultsWithThetaNPriors the pNonRef result for each allele independently
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*/
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protected AFCalculationResult combineIndependentPNonRefs(final VariantContext vc,
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final List<AFCalculationResult> sortedResultsWithThetaNPriors) {
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final List<AFCalculationResult> sortedResultsWithThetaNPriors,
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final AFCalculationResult combinedAltAllelesResult) {
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int nEvaluations = 0;
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final int nAltAlleles = sortedResultsWithThetaNPriors.size();
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final int[] alleleCountsOfMLE = new int[nAltAlleles];
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final double[] log10PriorsOfAC = new double[2];
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final Map<Allele, Double> log10pRefByAllele = new HashMap<Allele, Double>(nAltAlleles);
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// the sum of the log10 posteriors for AF == 0 and AF > 0 to determine joint probs
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double log10PosteriorOfACEq0Sum = 0.0;
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double log10PosteriorOfACGt0Sum = 0.0;
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boolean anyPoly = false;
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for ( final AFCalculationResult sortedResultWithThetaNPriors : sortedResultsWithThetaNPriors ) {
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final Allele altAllele = sortedResultWithThetaNPriors.getAllelesUsedInGenotyping().get(1);
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final int altI = vc.getAlleles().indexOf(altAllele) - 1;
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@ -446,16 +492,6 @@ import java.util.*;
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// MLE of altI allele is simply the MLE of this allele in altAlleles
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alleleCountsOfMLE[altI] = sortedResultWithThetaNPriors.getAlleleCountAtMLE(altAllele);
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// the AF > 0 case requires us to store the normalized likelihood for later summation
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if ( sortedResultWithThetaNPriors.getLog10PosteriorOfAFGT0() > MIN_LOG10_CONFIDENCE_TO_INCLUDE_ALLELE_IN_POSTERIOR ) {
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anyPoly = true;
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log10PosteriorOfACEq0Sum += sortedResultWithThetaNPriors.getLog10PosteriorOfAFEq0();
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log10PriorsOfAC[0] += sortedResultWithThetaNPriors.getLog10PriorOfAFEq0();
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log10PriorsOfAC[1] += sortedResultWithThetaNPriors.getLog10PriorOfAFGT0();
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}
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log10PosteriorOfACGt0Sum += sortedResultWithThetaNPriors.getLog10PosteriorOfAFGT0();
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// bind pNonRef for allele to the posterior value of the AF > 0 with the new adjusted prior
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log10pRefByAllele.put(altAllele, sortedResultWithThetaNPriors.getLog10PosteriorOfAFEq0());
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@ -463,36 +499,32 @@ import java.util.*;
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nEvaluations += sortedResultWithThetaNPriors.nEvaluations;
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}
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// If no alleles were polymorphic, make sure we have the proper priors (the defaults) for likelihood calculation
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if ( ! anyPoly ) {
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log10PriorsOfAC[0] = sortedResultsWithThetaNPriors.get(0).getLog10PriorOfAFEq0();
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log10PriorsOfAC[1] = sortedResultsWithThetaNPriors.get(0).getLog10PriorOfAFGT0();
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}
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// In principle, if B_p = x and C_p = y are the probabilities of being poly for alleles B and C,
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// the probability of being poly is (1 - B_p) * (1 - C_p) = (1 - x) * (1 - y). We want to estimate confidently
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// log10((1 - x) * (1 - y)) which is log10(1 - x) + log10(1 - y). This sum is log10PosteriorOfACEq0
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//
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// note we need to handle the case where the posterior of AF == 0 is 0.0, in which case we
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// use the summed log10PosteriorOfACGt0Sum directly. This happens in cases where
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// AF > 0 : 0.0 and AF == 0 : -16, and if you use the inverse calculation you get 0.0 and MathUtils.LOG10_P_OF_ZERO
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final double log10PosteriorOfACGt0;
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if ( log10PosteriorOfACEq0Sum == 0.0 )
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log10PosteriorOfACGt0 = log10PosteriorOfACGt0Sum;
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else
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log10PosteriorOfACGt0 = Math.max(Math.log10(1 - Math.pow(10, log10PosteriorOfACEq0Sum)), MathUtils.LOG10_P_OF_ZERO);
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final double[] log10LikelihoodsOfAC = new double[] {
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// L + prior = posterior => L = poster - prior
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log10PosteriorOfACEq0Sum - log10PriorsOfAC[0],
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log10PosteriorOfACGt0 - log10PriorsOfAC[1]
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};
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return new MyAFCalculationResult(alleleCountsOfMLE, nEvaluations, vc.getAlleles(),
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// necessary to ensure all values < 0
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MathUtils.normalizeFromLog10(log10LikelihoodsOfAC, true),
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MathUtils.normalizeFromLog10(new double[] { combinedAltAllelesResult.getLog10LikelihoodOfAFEq0(), combinedAltAllelesResult.getLog10LikelihoodOfAFGT0() }, true),
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// priors incorporate multiple alt alleles, must be normalized
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MathUtils.normalizeFromLog10(log10PriorsOfAC, true),
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MathUtils.normalizeFromLog10(new double[] { combinedAltAllelesResult.getLog10PriorOfAFEq0(), combinedAltAllelesResult.getLog10PriorOfAFGT0() }, true),
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log10pRefByAllele, sortedResultsWithThetaNPriors);
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}
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private boolean combineAltAlleleLikelihoods(final Genotype g, final int plMaxIndex, final double[] dest,
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final double[] hetLikelihoods, final double[] homAltLikelihoods) {
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final int[] pls = g.getPL();
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if (pls == null)
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return false;
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int hetNextIndex = 0;
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int homAltNextIndex = 0;
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for (int plIndex = 1; plIndex < plMaxIndex; plIndex++) {
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final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(plIndex);
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if (alleles.alleleIndex1 == 0 || alleles.alleleIndex2 == 0)
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hetLikelihoods[hetNextIndex++] = pls[plIndex] * PHRED_2_LOG10_COEFF;
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else
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homAltLikelihoods[homAltNextIndex++] = pls[plIndex] * PHRED_2_LOG10_COEFF;
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}
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dest[0] = pls[0] * PHRED_2_LOG10_COEFF;
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dest[1] = MathUtils.approximateLog10SumLog10(hetLikelihoods);
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dest[2] = MathUtils.approximateLog10SumLog10(homAltLikelihoods);
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return true;
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}
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}
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@ -135,7 +135,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
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"low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1,
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Arrays.asList("34a92dd832bbb8ed53abf21ba88c6faa"));
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Arrays.asList("053913cb29fee481158e1f497a4fffdc"));
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executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
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}
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@ -65,7 +65,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testMultiSamplePilot1() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
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Arrays.asList("a15a28d854789c71ef2879dd4c606b1a"));
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Arrays.asList("b43bf9147e30cc68068a91a5e8405767"));
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executeTest("test MultiSample Pilot1", spec);
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}
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@ -97,7 +97,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testMultipleSNPAlleles() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
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Arrays.asList("1a36b5c036e0452f526dc1a5fdd60929"));
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Arrays.asList("37594ce48695bf443c9251f70006f2f0"));
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executeTest("test Multiple SNP alleles", spec);
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}
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@ -113,7 +113,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testReverseTrim() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
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Arrays.asList("451a6a39d74bd3cc367da80f76b2f98d"));
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Arrays.asList("ad2be9f69ae8c6776b3bfba069735f50"));
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executeTest("test reverse trim", spec);
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}
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@ -121,7 +121,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testMismatchedPLs() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
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Arrays.asList("a3b299d1dd256fec5425e4175f747bfe"));
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Arrays.asList("1cc9c3e45e0296bb33042b409db18ca4"));
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executeTest("test mismatched PLs", spec);
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}
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}
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@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
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@Test
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public void testHaplotypeCallerMultiSampleComplex1() {
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HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "29f216779f0db9a08f4907ea82f0c7fb");
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HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "f4018f734d64f1f88b3ac4b712311567");
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}
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private void HCTestSymbolicVariants(String bam, String args, String md5) {
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@ -85,9 +85,9 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
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final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
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// this functionality can be adapted to provide input data for whatever you might want in your data
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tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "f8bc02b296d89369fe7ddf3923743c26"});
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tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "ad0b6274991d451a6491f3118f0e7b2b"});
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tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "956938fd1b5c7bf1b717326a7dd46d91"});
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tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "0a982ba98be666d56452791df32109d7"});
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tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "5edcfa5ab96bc327783484c2bbe1c06f"});
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tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "b60c70fac56f129af78eaff9ad769557"});
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tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "1c3570461e96ad6d66c6abb0fd6ee865"});
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tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "66019a0914f905522da6bd3b557a57d1"});
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@ -218,7 +218,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
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public void testNoCallGVCFMissingPLsBugFix() {
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final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
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b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
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final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("187e43b1034478edced1eb5c664bac34"));
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final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("7ef1f30d92178f75e5220b16508b47cd"));
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spec.disableShadowBCF();
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executeTest("testNoCallGVCFMissingPLsBugFix", spec);
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}
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@ -85,12 +85,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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@Test
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public void testHaplotypeCallerMultiSample() {
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HCTest(CEUTRIO_BAM, "", "7bc718c6a604405e6d33c3073630cc66");
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HCTest(CEUTRIO_BAM, "", "5468f50b4ed198e6e9b05a67c3103f72");
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}
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@Test
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public void testHaplotypeCallerSingleSample() {
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HCTest(NA12878_BAM, "", "07125724eb465a739df9c6ab191216b0");
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HCTest(NA12878_BAM, "", "e85ada8486a4ed7231918187a100e1c3");
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}
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@Test
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@ -111,7 +111,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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@Test
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public void testHaplotypeCallerMinBaseQuality() {
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HCTest(NA12878_BAM, "-mbq 15", "07125724eb465a739df9c6ab191216b0");
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HCTest(NA12878_BAM, "-mbq 15", "e85ada8486a4ed7231918187a100e1c3");
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}
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@Test
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@ -126,7 +126,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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@Test
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public void testHaplotypeCallerGraphBasedSingleSample() {
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HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "79b0f8fa5e42ef23f3d166d84d92fa23");
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HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "129965453a3ad9a22aa241f8c4afcbbf");
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}
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@Test
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@ -136,19 +136,19 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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@Test
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public void testHaplotypeCallerGraphBasedMultiSample() {
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HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "10119fbb494e966a6f1b54307cfbeb8b");
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HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "987c0bb684fc03bcc46cb619e8269fe4");
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}
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@Test
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public void testHaplotypeCallerSingleSampleWithDbsnp() {
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HCTest(NA12878_BAM, "-D " + b37dbSNP132, "fded195a0436242673718e6dc083c172");
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HCTest(NA12878_BAM, "-D " + b37dbSNP132, "0f9f45384669cde243731ca803fa3a0b");
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}
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@Test
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public void testHaplotypeCallerMultiSampleGGA() {
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HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf" +
|
||||
" -isr INTERSECTION -L " + GGA_INTERVALS_FILE,
|
||||
"5bc8892b68e281a3ceb4f2d141f8c723");
|
||||
"86a060e9514eaf90c14ddaa7e6d07259");
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
|||
|
|
@ -60,7 +60,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
|
|||
List<Object[]> tests = new ArrayList<>();
|
||||
|
||||
for ( final int nct : Arrays.asList(1, 2, 4) ) {
|
||||
tests.add(new Object[]{nct, "faaf2217a920225b6937d87e949d1a68"});
|
||||
tests.add(new Object[]{nct, "8bcf149228e8845915733d6fd889a141"});
|
||||
}
|
||||
|
||||
return tests.toArray(new Object[][]{});
|
||||
|
|
|
|||
|
|
@ -66,7 +66,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference),
|
||||
1,
|
||||
Arrays.asList("bc3d3eff337836af245b81f52b94d70c"));
|
||||
Arrays.asList("27bc40f7cc46bdc347284d7522b2aa6c"));
|
||||
executeTest("testUpdatePGT", spec);
|
||||
}
|
||||
|
||||
|
|
@ -78,7 +78,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
|
||||
" -L 20:10,000,000-20,000,000", b37KGReference),
|
||||
1,
|
||||
Arrays.asList("9d9ddeb831e5512c5b1084ee22e65459"));
|
||||
Arrays.asList("bb7775a555ee9859e18a28cbc044a160"));
|
||||
executeTest("combineSingleSamplePipelineGVCF", spec);
|
||||
}
|
||||
|
||||
|
|
@ -127,7 +127,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
|
||||
" -L 20:10,000,000-20,000,000", b37KGReference),
|
||||
1,
|
||||
Arrays.asList("aa0f9604bb496be143a6dde775e157fe"));
|
||||
Arrays.asList("9b7f2ba1bde2e0a0eb3ebc0afb6bc513"));
|
||||
executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
|
||||
}
|
||||
|
||||
|
|
@ -139,7 +139,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
|
||||
" -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
|
||||
1,
|
||||
Arrays.asList("49f8ff728246d08cd20cd1c1521651f9"));
|
||||
Arrays.asList("8201cee7120dfdb3fdeace0ec511c7b1"));
|
||||
executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
|
||||
}
|
||||
|
||||
|
|
@ -186,7 +186,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseBPResolutionString("-nda"),
|
||||
1,
|
||||
Arrays.asList("27cddeb2287827a58d79fc7d3ddad080"));
|
||||
Arrays.asList("d50e5035488f63c574dcb8485ff61fcb"));
|
||||
executeTest("testNDA", spec);
|
||||
}
|
||||
|
||||
|
|
@ -204,7 +204,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseBPResolutionString("-stand_call_conf 300 -stand_emit_conf 100"),
|
||||
1,
|
||||
Arrays.asList("c841b408e41596529009bf7f07de9b3f"));
|
||||
Arrays.asList("bd58c026e9c8df4d4166f22cd0f0ce65"));
|
||||
executeTest("testStandardConf", spec);
|
||||
}
|
||||
}
|
||||
|
|
@ -65,9 +65,7 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
|
|||
|
||||
for ( final int nt : Arrays.asList(1, 2) )
|
||||
for ( final int nct : Arrays.asList(1, 2) ) {
|
||||
// tests.add(new Object[]{ "SNP", "a1c7546f32a8919a3f3a70a04b2e8322", nt, nct });
|
||||
//// tests.add(new Object[]{ "INDEL", "0a6d2be79f4f8a4b0eb788cc4751b31b", nt, nct });
|
||||
tests.add(new Object[]{ "BOTH", "392dc99dc279082fc6e729b249adfa2b", nt, nct });
|
||||
tests.add(new Object[]{ "BOTH", "18418ddc2bdbe20c38ece6dd18535be7", nt, nct });
|
||||
}
|
||||
|
||||
return tests.toArray(new Object[][]{});
|
||||
|
|
@ -79,7 +77,6 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
|
|||
buildCommandLine(
|
||||
"-T UnifiedGenotyper -R " + b37KGReference,
|
||||
"--no_cmdline_in_header -G none",
|
||||
//"--dbsnp " + b37dbSNP132,
|
||||
"-I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam",
|
||||
"-L 20:10,000,000-10,100,000",
|
||||
"-glm " + glm,
|
||||
|
|
|
|||
Loading…
Reference in New Issue