37 lines
5.0 KiB
Plaintext
37 lines
5.0 KiB
Plaintext
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##:GATKReport.v0.1 CompOverlap : The overlap between eval and comp sites
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CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants nCompVariants novelSites nVariantsAtComp compRate nConcordant concordantRate
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CompOverlap none eval none all 0 0 0 0 0.00000000 0 0.00000000
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CompOverlap none eval none known 0 0 0 0 0.00000000 0 0.00000000
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CompOverlap none eval none novel 0 0 0 0 0.00000000 0 0.00000000
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##:GATKReport.v0.1 CountVariants : Counts different classes of variants in the sample
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CountVariants CompRod EvalRod JexlExpression Novelty nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nNoCalls nHets nHomRef nHomVar nSingletons heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp deletionInsertionRatio
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CountVariants none eval none all 100000 100000 100000 0 0.00000000 0.00000000 0 0 0 0 0 99872 0 128 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
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CountVariants none eval none known 100000 0 0 0 0.00000000 0.00000000 0 0 0 0 0 0 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
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CountVariants none eval none novel 100000 100000 100000 0 0.00000000 0.00000000 0 0 0 0 0 99872 0 128 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
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##:GATKReport.v0.1 SimpleMetricsByAC.metrics : TiTv by allele count
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SimpleMetricsByAC.metrics CompRod EvalRod JexlExpression Novelty row AC nTi nTv n TiTv
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SimpleMetricsByAC.metrics none eval none all ac0 0 0 0 0 0.0
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SimpleMetricsByAC.metrics none eval none all ac1 1 0 0 0 0.0
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SimpleMetricsByAC.metrics none eval none all ac2 2 0 0 0 0.0
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SimpleMetricsByAC.metrics none eval none known ac0 0 0 0 0 0.0
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SimpleMetricsByAC.metrics none eval none known ac1 1 0 0 0 0.0
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SimpleMetricsByAC.metrics none eval none known ac2 2 0 0 0 0.0
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SimpleMetricsByAC.metrics none eval none novel ac0 0 0 0 0 0.0
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SimpleMetricsByAC.metrics none eval none novel ac1 1 0 0 0 0.0
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SimpleMetricsByAC.metrics none eval none novel ac2 2 0 0 0 0.0
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##:GATKReport.v0.1 TiTvVariantEvaluator : Ti/Tv Variant Evaluator
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TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard
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TiTvVariantEvaluator none eval none all 0 0 0.00000000 0 0 0.00000000
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TiTvVariantEvaluator none eval none known 0 0 0.00000000 0 0 0.00000000
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TiTvVariantEvaluator none eval none novel 0 0 0.00000000 0 0 0.00000000
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##:GATKReport.v0.1 ValidationReport : Assess site accuracy and sensitivity of callset against follow-up validation assay
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ValidationReport CompRod EvalRod JexlExpression Novelty nComp TP FP FN TN sensitivity PPV FDR CompMonoEvalNoCall CompMonoEvalFiltered CompMonoEvalMono CompMonoEvalPoly CompPolyEvalNoCall CompPolyEvalFiltered CompPolyEvalMono CompPolyEvalPoly CompFiltered nDifferentAlleleSites
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ValidationReport none eval none all 0 0 0 0 0 NaN NaN NaN 0 0 0 0 0 0 0 0 0 0
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ValidationReport none eval none known 0 0 0 0 0 NaN NaN NaN 0 0 0 0 0 0 0 0 0 0
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ValidationReport none eval none novel 0 0 0 0 0 NaN NaN NaN 0 0 0 0 0 0 0 0 0 0
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