/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular
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- ##:GATKReport.v0.1 CompOverlap : The overlap between eval and comp sites
- CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants nCompVariants novelSites nVariantsAtComp compRate nConcordant concordantRate
- CompOverlap dbsnp eval none all 0 0 0 0 0.00000000 0 0.00000000
- CompOverlap dbsnp eval none known 0 0 0 0 0.00000000 0 0.00000000
- CompOverlap dbsnp eval none novel 0 0 0 0 0.00000000 0 0.00000000
- ##:GATKReport.v0.1 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 nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp deletionInsertionRatio
- CountVariants dbsnp eval none all 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
- CountVariants dbsnp eval none known 5386 0 0 0 0.00000000 0.00000000 0 0 0 0 0 0 0 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
- CountVariants dbsnp eval none novel 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
- ##:GATKReport.v0.1 SimpleMetricsByAC.metrics : TiTv by allele count
- SimpleMetricsByAC.metrics CompRod EvalRod JexlExpression Novelty row AC nTi nTv n TiTv
- SimpleMetricsByAC.metrics dbsnp eval none all ac0 0 0 0 0 0.0
- SimpleMetricsByAC.metrics dbsnp eval none all ac1 1 0 0 0 0.0
- SimpleMetricsByAC.metrics dbsnp eval none all ac2 2 0 0 0 0.0
- SimpleMetricsByAC.metrics dbsnp eval none known ac0 0 0 0 0 0.0
- SimpleMetricsByAC.metrics dbsnp eval none known ac1 1 0 0 0 0.0
- SimpleMetricsByAC.metrics dbsnp eval none known ac2 2 0 0 0 0.0
- SimpleMetricsByAC.metrics dbsnp eval none novel ac0 0 0 0 0 0.0
- SimpleMetricsByAC.metrics dbsnp eval none novel ac1 1 0 0 0 0.0
- SimpleMetricsByAC.metrics dbsnp eval none novel ac2 2 0 0 0 0.0
- ##:GATKReport.v0.1 TiTvVariantEvaluator : Ti/Tv Variant Evaluator
- TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard nTiDerived nTvDerived tiTvDerivedRatio
- TiTvVariantEvaluator dbsnp eval none all 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000
- TiTvVariantEvaluator dbsnp eval none known 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000
- TiTvVariantEvaluator dbsnp eval none novel 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000
- ##:GATKReport.v0.1 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 eval none all 0 0 0 0 0 NaN 100.00000000 NaN NaN 0 0 0 0 0 0 0 0 0 0
- ValidationReport dbsnp eval none known 0 0 0 0 0 NaN 100.00000000 NaN NaN 0 0 0 0 0 0 0 0 0 0
- ValidationReport dbsnp eval none novel 0 0 0 0 0 NaN 100.00000000 NaN NaN 0 0 0 0 0 0 0 0 0 0