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galaxy-obo / test-data / gatk / gatk_variant_eval / gatk_variant_eval_out_1.gatk_report

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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