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view test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report @ 0:340633249b3d draft
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| author | bgruening |
|---|---|
| date | Mon, 02 Dec 2013 06:18:36 -0500 |
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##:GATKReport.v0.2 CompOverlap : The overlap between eval and comp sites CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants novelSites nVariantsAtComp compRate nConcordant concordantRate CompOverlap dbsnp input_0 none all 0 0 0 0.00 0 0.00 CompOverlap dbsnp input_0 none known 0 0 0 0.00 0 0.00 CompOverlap dbsnp input_0 none novel 0 0 0 0.00 0 0.00 ##:GATKReport.v0.2 CountVariants : Counts different classes of variants in the sample CountVariants CompRod EvalRod JexlExpression Novelty nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nSymbolic nMixed nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp deletionInsertionRatio CountVariants dbsnp input_0 none all 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 CountVariants dbsnp input_0 none known 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 CountVariants dbsnp input_0 none novel 5386 0 0 0 0.00000000 0.00000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 ##:GATKReport.v0.2 TiTvVariantEvaluator : Ti/Tv Variant Evaluator TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard nTiDerived nTvDerived tiTvDerivedRatio TiTvVariantEvaluator dbsnp input_0 none all 0 0 0.00 0 0 0.00 0 0 0.00 TiTvVariantEvaluator dbsnp input_0 none known 0 0 0.00 0 0 0.00 0 0 0.00 TiTvVariantEvaluator dbsnp input_0 none novel 0 0 0.00 0 0 0.00 0 0 0.00 ##:GATKReport.v0.2 ValidationReport : Assess site accuracy and sensitivity of callset against follow-up validation assay ValidationReport CompRod EvalRod JexlExpression Novelty nComp TP FP FN TN sensitivity specificity PPV FDR CompMonoEvalNoCall CompMonoEvalFiltered CompMonoEvalMono CompMonoEvalPoly CompPolyEvalNoCall CompPolyEvalFiltered CompPolyEvalMono CompPolyEvalPoly CompFiltered nDifferentAlleleSites ValidationReport dbsnp input_0 none all 43 0 0 0 43 NaN 100.00 NaN NaN 42 0 1 0 0 0 0 0 0 0 ValidationReport dbsnp input_0 none known 1 0 0 0 1 NaN 100.00 NaN NaN 0 0 1 0 0 0 0 0 0 0 ValidationReport dbsnp input_0 none novel 42 0 0 0 42 NaN 100.00 NaN NaN 42 0 0 0 0 0 0 0 0 0 ##:GATKReport.v0.2 VariantSummary : 1000 Genomes Phase I summary of variants table VariantSummary CompRod EvalRod JexlExpression Novelty nSamples nProcessedLoci nSNPs TiTvRatio SNPNoveltyRate nSNPsPerSample TiTvRatioPerSample SNPDPPerSample nIndels IndelNoveltyRate nIndelsPerSample IndelDPPerSample nSVs SVNoveltyRate nSVsPerSample VariantSummary dbsnp input_0 none all 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 VariantSummary dbsnp input_0 none known 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 VariantSummary dbsnp input_0 none novel 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0