37 lines
5.8 KiB
Plaintext
37 lines
5.8 KiB
Plaintext
#:GATKReport.v1.1:5
|
|
#:GATKTable:11:3:%s:%s:%s:%s:%s:%s:%s:%s:%.2f:%s:%.2f
|
|
#:GATKTable:CompOverlap:The overlap between eval and comp sites
|
|
CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants novelSites nVariantsAtComp compRate nConcordant concordantRate
|
|
CompOverlap dbsnp eval none all 481 12 469 97.51 468 99.79
|
|
CompOverlap dbsnp eval none known 469 0 469 100.00 468 99.79
|
|
CompOverlap dbsnp eval none novel 12 12 0 0.00 0 0.00
|
|
|
|
#:GATKTable:30:3:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%.2e:%.2f:%.2f:%.2e:%.2f:%.2f
|
|
#:GATKTable: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 eval none all 63025520 481 0 481 7.63182913841885E-6 131030.0 481 0 0 0 0 0 0 0 298 0 183 298 0 4.73e-06 211495.00 1.63 0.00e+00 0.00 0.00
|
|
CountVariants dbsnp eval none known 63025520 469 0 469 7.441430074674513E-6 134382.0 469 0 0 0 0 0 0 0 288 0 181 288 0 4.57e-06 218838.00 1.59 0.00e+00 0.00 0.00
|
|
CountVariants dbsnp eval none novel 63025520 12 0 12 1.9039906374433722E-7 5252126.0 12 0 0 0 0 0 0 0 10 0 2 10 0 1.59e-07 6302552.00 5.00 0.00e+00 0.00 0.00
|
|
|
|
#:GATKTable:14:3:%s:%s:%s:%s:%s:%s:%s:%.2f:%s:%s:%.2f:%s:%s:%.2f
|
|
#:GATKTable:TiTvVariantEvaluator:Ti/Tv Variant Evaluator
|
|
TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard nTiDerived nTvDerived tiTvDerivedRatio
|
|
TiTvVariantEvaluator dbsnp eval none all 382 99 3.86 203506 85497 2.38 0 0 0.00
|
|
TiTvVariantEvaluator dbsnp eval none known 374 95 3.94 360 91 3.96 0 0 0.00
|
|
TiTvVariantEvaluator dbsnp eval none novel 8 4 2.00 203146 85406 2.38 0 0 0.00
|
|
|
|
#:GATKTable:24:3:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%.2f:%.2f:%.2f:%.2f:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s
|
|
#:GATKTable: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 369102 469 0 368633 0 0.13 100.00 100.00 0.00 0 0 0 0 368633 0 0 469 0 0
|
|
ValidationReport dbsnp eval none known 469 469 0 0 0 100.00 100.00 100.00 0.00 0 0 0 0 0 0 0 469 0 0
|
|
ValidationReport dbsnp eval none novel 368633 0 0 368633 0 0.00 100.00 NaN NaN 0 0 0 0 368633 0 0 0 0 0
|
|
|
|
#:GATKTable:20:3:%s:%s:%s:%s:%s:%s:%s:%s:%.2f:%s:%s:%.2f:%.1f:%s:%s:%s:%.1f:%s:%s:%s
|
|
#:GATKTable: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 eval none all 1 63025520 481 3.86 0.02 481 3.86 481.0 0 NA 0 0.0 0 NA 0
|
|
VariantSummary dbsnp eval none known 1 63025520 469 3.94 0.00 469 3.94 469.0 0 NA 0 0.0 0 NA 0
|
|
VariantSummary dbsnp eval none novel 1 63025520 12 2.00 1.00 12 2.00 12.0 0 NA 0 0.0 0 NA 0
|
|
|