public void VennVcf_CombineTwoPoolVariants_Qscore_Test() { //Var A, kdot-43_S3.genome.vcf //chr3 41266161 . A G 30 PASS DP=3067 GT:GQ:AD:VF:NL:SB 0/1:30:3005,54:0.0176:35:-100.0000 CalledAllele VarA = new CalledAllele(); VarA.Chromosome = "chr3"; VarA.ReferencePosition = 41266161; VarA.TotalCoverage = 3067; VarA.Genotype = Pisces.Domain.Types.Genotype.HeterozygousAltRef; VarA.GenotypeQscore = 30; VarA.AlleleSupport = 54; VarA.ReferenceSupport = 3005; // "VF", "0.0176" VarA.NoiseLevelApplied = 35; VarA.StrandBiasResults = new Pisces.Domain.Models.BiasResults() { GATKBiasScore = -100 }; VarA.ReferenceAllele = "A"; VarA.AlternateAllele = "G"; VarA.Filters = new List <Pisces.Domain.Types.FilterType>(); VarA.VariantQscore = 30; VarA.Type = Pisces.Domain.Types.AlleleCategory.Snv; //Var B, kdot-43_S4.genome.vcf //chr3 41266161 . A . 75 PASS DP=3795 GT:GQ:AD:VF:NL:SB 0/0:75:3780:0.0040:35:-100.0000 CalledAllele VarB = new CalledAllele(); VarB.Chromosome = "chr3"; VarB.ReferencePosition = 41266161; VarB.TotalCoverage = 3795; VarB.Genotype = Pisces.Domain.Types.Genotype.HomozygousRef; VarB.GenotypeQscore = 75; VarB.AlleleSupport = 3780; VarB.ReferenceSupport = 3780; // "VF", "0.0040" VarB.NoiseLevelApplied = 35; VarB.StrandBiasResults = new Pisces.Domain.Models.BiasResults() { GATKBiasScore = -100 }; VarB.ReferenceAllele = "A"; VarB.AlternateAllele = "."; VarB.Filters = new List <Pisces.Domain.Types.FilterType>(); VarB.VariantQscore = 75; VarB.Type = Pisces.Domain.Types.AlleleCategory.Reference; //old answer //chr3 41266161 . A . 100.00 PASS DP=6862;cosmic=COSM1423020,COSM1423021;EVS=0|69.0|6503;phastCons GT:GQ:AD:VF:NL:SB:PB:GQX 0/0:100:6785:0.0079:35:-100:-100.0000:100 VennVcfOptions parameters = new VennVcfOptions(); parameters.VariantCallingParams.MinimumFrequencyFilter = 0.03f; parameters.VariantCallingParams.MinimumFrequency = 0.01f; parameters.BamFilterParams.MinimumBaseCallQuality = 20; parameters.SampleAggregationParameters.ProbePoolBiasThreshold = 0.5f; parameters.SampleAggregationParameters.HowToCombineQScore = SampleAggregationParameters.CombineQScoreMethod.TakeMin; VariantComparisonCase ComparisonCase = VennProcessor.GetComparisonCase(VarA, VarB); ConsensusBuilder consensusBuilder = new ConsensusBuilder("", parameters); AggregateAllele consensus = consensusBuilder.CombineVariants(VarA, VarB, ComparisonCase); //GT:GQ:AD:VF:NL:SB:PB:GQX 0/0:100:6785:0.0079:35:-100:-100.0000:100 Assert.NotNull(consensus); Assert.Equal(consensus.VariantQscore, 100); Assert.Equal(consensus.GenotypeQscore, 100); Assert.Equal(consensus.ReferenceAllele, "A"); Assert.Equal(consensus.AlternateAllele, "."); Assert.Equal(consensus.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef); Assert.Equal(consensus.GenotypeQscore, 100); Assert.Equal(consensus.AlleleSupport, 6785); Assert.Equal(consensus.ReferenceSupport, 6785); Assert.Equal(consensus.TotalCoverage, 6862); Assert.Equal(consensus.Frequency, 0.98877, 4); Assert.Equal(consensus.NoiseLevelApplied, 35); Assert.Equal(consensus.StrandBiasResults.GATKBiasScore, -100); Assert.Equal(consensus.PoolBiasResults.GATKBiasScore, -100); }
public void VennVcf_CombineTwoPoolVariants_Qscore_DiffentNL_Test() { //chr3 41266161 . A G 30 PASS DP=3067 GT:GQ:AD:VF:NL:SB 0/1:30:3005,54:0.0176:35:-100.0000 CalledAllele VarA = new CalledAllele() { Chromosome = "chr3", ReferencePosition = 41266161, TotalCoverage = 3067, Genotype = Pisces.Domain.Types.Genotype.HeterozygousAltRef, VariantQscore = 30, GenotypeQscore = 30, AlleleSupport = 54, ReferenceSupport = 3005, NoiseLevelApplied = 35, StrandBiasResults = new Pisces.Domain.Models.BiasResults() { GATKBiasScore = -100.0000 }, ReferenceAllele = "A", AlternateAllele = "G", Type = Pisces.Domain.Types.AlleleCategory.Snv }; ///chr3 41266161 . A . 75 PASS DP=3795 GT:GQ:AD:VF:NL:SB 0/0:75:3780:0.0040:2:-100.0000 CalledAllele VarB = new CalledAllele() { Chromosome = "chr3", ReferencePosition = 41266161, TotalCoverage = 3795, Genotype = Pisces.Domain.Types.Genotype.HomozygousRef, VariantQscore = 75, GenotypeQscore = 75, AlleleSupport = 3780, ReferenceSupport = 3780, NoiseLevelApplied = 2, StrandBiasResults = new Pisces.Domain.Models.BiasResults() { GATKBiasScore = -100.0000 }, ReferenceAllele = "A", AlternateAllele = ".", Type = Pisces.Domain.Types.AlleleCategory.Reference }; //old answer //chr3 41266161 . A . 100.00 PASS DP=6862;cosmic=COSM1423020,COSM1423021;EVS=0|69.0|6503;phastCons GT:GQ:AD:VF:NL:SB:PB:GQX 0/0:100:6785:0.0079:35:-100:-100.0000:100 SampleAggregationParameters SampleAggregationOptions = new SampleAggregationParameters(); SampleAggregationOptions.ProbePoolBiasThreshold = 0.5f; SampleAggregationOptions.HowToCombineQScore = SampleAggregationParameters.CombineQScoreMethod.CombinePoolsAndReCalculate; _basicOptions.BamFilterParams.MinimumBaseCallQuality = 20; _basicOptions.VariantCallingParams.MinimumFrequency = 0.01f; _basicOptions.VariantCallingParams.MinimumFrequencyFilter = 0.03f; _basicOptions.SampleAggregationParameters = SampleAggregationOptions; string consensusOut = Path.Combine(_TestDataPath, "ConsensusOut.vcf"); VariantComparisonCase ComparisonCase = VennProcessor.GetComparisonCase(VarA, VarB); ConsensusBuilder consensusBuilder = new ConsensusBuilder(consensusOut, _basicOptions); AggregateAllele consensus = consensusBuilder.CombineVariants(VarA, VarB, ComparisonCase); Console.WriteLine(consensus.ToString()); double expectedNoiseLevel = MathOperations.PtoQ( (MathOperations.QtoP(35) + MathOperations.QtoP(2)) / (2.0)); // 5 //GT:GQ:AD:VF:NL:SB:PB:GQX 0/0:100:6785:0.0079:35:-100:-100.0000:100 Assert.NotNull(consensus); Assert.Equal(consensus.VariantQscore, 100); Assert.Equal(consensus.ReferenceAllele, "A"); Assert.Equal(consensus.AlternateAllele, "."); Assert.Equal(consensus.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef); Assert.Equal(consensus.TotalCoverage, 6862); Assert.Equal(consensus.ReferenceSupport, 6785); Assert.Equal(consensus.AlleleSupport, 6785); Assert.Equal(consensus.GenotypeQscore, 100); Assert.Equal(consensus.Frequency, 0.98877877f); Assert.Equal(consensus.NoiseLevelApplied, ((int)expectedNoiseLevel)); Assert.Equal(consensus.NoiseLevelApplied, 5); Assert.Equal(consensus.StrandBiasResults.GATKBiasScore, -100); Assert.Equal(consensus.PoolBiasResults.GATKBiasScore, -100.0000); //now check, we take the min NL score if we are taking the min Q score. // (in this case of combined alt+ref -> ref, the q score will still need to be recalculated. //just with the MIN NL. SampleAggregationOptions.HowToCombineQScore = SampleAggregationParameters.CombineQScoreMethod.TakeMin; ComparisonCase = VennProcessor.GetComparisonCase(VarA, VarB); consensus = consensusBuilder.CombineVariants(VarA, VarB, ComparisonCase); Assert.Equal(consensus.NoiseLevelApplied, 2); Assert.Equal(consensus.VariantQscore, 100); //ok, now sanity check we dont barf if either input is null: ComparisonCase = VennProcessor.GetComparisonCase(VarA, null); consensus = consensusBuilder.CombineVariants(VarA, null, ComparisonCase); Assert.Equal(consensus.NoiseLevelApplied, 35); Assert.Equal(consensus.VariantQscore, 100); ComparisonCase = VennProcessor.GetComparisonCase(null, VarB); consensus = consensusBuilder.CombineVariants(null, VarB, ComparisonCase); Assert.Equal(consensus.NoiseLevelApplied, 2); Assert.Equal(consensus.VariantQscore, 100); //ok, lets check this again, for the PoolQScores option. //sanity check we dont barf if either input is null: SampleAggregationOptions.HowToCombineQScore = SampleAggregationParameters.CombineQScoreMethod.CombinePoolsAndReCalculate; ComparisonCase = VennProcessor.GetComparisonCase(VarA, null); consensus = consensusBuilder.CombineVariants(VarA, null, ComparisonCase); Assert.Equal(consensus.NoiseLevelApplied, 35); Assert.Equal(consensus.VariantQscore, 100);//low freq variant -> nocall. note, qscore would be 41 if NL = 20. ComparisonCase = VennProcessor.GetComparisonCase(null, VarB); consensus = consensusBuilder.CombineVariants(null, VarB, ComparisonCase); Assert.Equal(consensus.NoiseLevelApplied, 2); Assert.Equal(consensus.VariantQscore, 100); //sold ref }
public void VennVcf_CombineTwoPoolVariants_RulesAthroughD_Tests() { var outDir = TestPaths.LocalScratchDirectory; var VcfPathRoot = _TestDataPath; string OutputPath = Path.Combine(outDir, "outEandF.vcf"); if (File.Exists(OutputPath)) { File.Delete(OutputPath); } VennVcfOptions parameters = new VennVcfOptions(); parameters.VariantCallingParams.MinimumFrequencyFilter = 0.03f; parameters.VariantCallingParams.MinimumFrequency = 0.01f; parameters.ConsensusFileName = OutputPath; string VcfPath_PoolA = Path.Combine(VcfPathRoot, "09H-03403-MT1-1_S7.genome.vcf"); var PoolAVariants = (AlleleReader.GetAllVariantsInFile(VcfPath_PoolA)).ToList(); string VcfPath_PoolB = Path.Combine(VcfPathRoot, "09H-03403-MT1-1_S8.genome.vcf"); var PoolBVariants = (AlleleReader.GetAllVariantsInFile(VcfPath_PoolB)).ToList(); CalledAllele VariantA = PoolAVariants[0]; CalledAllele VariantB = PoolBVariants[0]; List <CalledAllele[]> pairs = VennProcessor.SelectPairs( new List <CalledAllele>() { VariantA }, new List <CalledAllele> { VariantB }); VariantComparisonCase ComparisonCase = VennProcessor.GetComparisonCase(pairs[0][0], pairs[0][1]); ConsensusBuilder consensusBuilder = new ConsensusBuilder("", parameters); CalledAllele Consensus = consensusBuilder.CombineVariants( VariantA, VariantB, ComparisonCase); //Rule "A" test //A if combined VF<1% and less than 2.6% in each pool, call REF //(note, we were Alt in one pool and ref in another) Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef); Assert.Equal(VariantA.Frequency, 0.9979, 4); Assert.Equal(VariantA.VariantQscore, 100); Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> { }); Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef); Assert.Equal(VariantB.Frequency, 0.0173, 4); Assert.Equal(VariantB.VariantQscore, 100); Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> { }); Assert.Equal(ComparisonCase, VariantComparisonCase.OneReferenceOneAlternate); Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef); Assert.Equal(Consensus.Frequency, 0.9907, 4); Assert.Equal(Consensus.VariantQscore, 100); Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> { }); //<-low VF tag will NOT added by post-processing b/c is ref call //B if combined VF<1% and more than 2.6% in one pool, call NO CALL VariantA = PoolAVariants[1]; VariantB = PoolBVariants[1]; ComparisonCase = VennProcessor.GetComparisonCase(VariantA, VariantB); Consensus = consensusBuilder.CombineVariants( VariantA, VariantB, ComparisonCase); Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef); Assert.Equal(VariantA.Frequency, 0.0776, 4); Assert.Equal(VariantA.VariantQscore, 100); Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> { }); Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef); Assert.Equal(VariantB.Frequency, 0.9989, 4); Assert.Equal(VariantB.VariantQscore, 100); Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> { }); Assert.Equal(ComparisonCase, VariantComparisonCase.OneReferenceOneAlternate); Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.AltLikeNoCall); Assert.Equal(Consensus.Frequency, 0.0070, 4); Assert.Equal(Consensus.VariantQscore, 0); Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> { Pisces.Domain.Types.FilterType.PoolBias }); //<-low VF tag will also get added by post-processing //Rule "Ca" test //C-a if combined 1%<VF<2.6% // and more than 2.6% in one pool and less than 1% in the other, call NO CALL w/PB VariantA = PoolAVariants[2]; VariantB = PoolBVariants[2]; ComparisonCase = VennProcessor.GetComparisonCase(VariantA, VariantB); Consensus = consensusBuilder.CombineVariants( VariantA, VariantB, ComparisonCase); Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef); Assert.Equal(VariantA.Frequency, 0.0367, 4); Assert.Equal(VariantA.VariantQscore, 100); Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> { }); Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef); Assert.Equal(VariantB.Frequency, 0.9976, 4); Assert.Equal(VariantB.VariantQscore, 100); Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> { }); Assert.Equal(ComparisonCase, VariantComparisonCase.OneReferenceOneAlternate); Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.AltLikeNoCall); Assert.Equal(Consensus.Frequency, 0.0117, 4); Assert.Equal(Consensus.VariantQscore, 23); Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> { Pisces.Domain.Types.FilterType.PoolBias }); //Rule "Cb" test //C-a if combined 1%<VF<2.6% // and more than 2.6% in one pool and between 1% and 2.6% in the other, call NO CALL w/ no PB VariantA = PoolAVariants[3]; VariantB = PoolBVariants[3]; ComparisonCase = VennProcessor.GetComparisonCase(VariantA, VariantB); Consensus = consensusBuilder.CombineVariants( VariantA, VariantB, ComparisonCase); Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef); Assert.Equal(VariantA.Frequency, 0.01725, 4); Assert.Equal(VariantA.VariantQscore, 100); Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> { }); Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef); Assert.Equal(VariantB.Frequency, 0.03667, 4); Assert.Equal(VariantB.VariantQscore, 100); Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> { }); Assert.Equal(ComparisonCase, VariantComparisonCase.AgreedOnAlternate); Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.AltLikeNoCall); Assert.Equal(Consensus.Frequency, 0.02347, 4); Assert.Equal(Consensus.VariantQscore, 100); Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> { }); //<-low VF tag will also get added by post-processing //Rule "D" test //D if combined VF>=2.6% call VARIANT (PB if only present in one pool, using 1% as the cutoff) VariantA = PoolAVariants[4]; VariantB = PoolBVariants[4]; ComparisonCase = VennProcessor.GetComparisonCase(VariantA, VariantB); Consensus = consensusBuilder.CombineVariants( VariantA, VariantB, ComparisonCase); Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef); Assert.Equal(VariantA.Frequency, 0.2509, 4); Assert.Equal(VariantA.VariantQscore, 100); Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> { }); Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef); Assert.Equal(VariantB.Frequency, 0.0367, 4); Assert.Equal(VariantB.VariantQscore, 100); Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> { }); Assert.Equal(ComparisonCase, VariantComparisonCase.AgreedOnAlternate); Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef); Assert.Equal(Consensus.Frequency, 0.1716, 4); Assert.Equal(Consensus.VariantQscore, 100); Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> { }); //<-low VF tag will also get set by post processor }