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/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular

https://bitbucket.org/cistrome/cistrome-harvard/
Unknown | 36 lines | 31 code | 5 blank | 0 comment | 0 complexity | 9f3c0bd9f6f9a753f4ef9a57915a7aeb MD5 | raw file
 1##:GATKReport.v0.1 CompOverlap : The overlap between eval and comp sites
 2CompOverlap  CompRod  EvalRod  JexlExpression  Novelty  nEvalVariants  nCompVariants  novelSites  nVariantsAtComp  compRate  nConcordant  concordantRate
 3CompOverlap  dbsnp    eval     none            all      0              0              0           0                0.00000000  0            0.00000000    
 4CompOverlap  dbsnp    eval     none            known    0              0              0           0                0.00000000  0            0.00000000    
 5CompOverlap  dbsnp    eval     none            novel    0              0              0           0                0.00000000  0            0.00000000    
 6
 7##:GATKReport.v0.1 CountVariants : Counts different classes of variants in the sample
 8CountVariants  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
 9CountVariants  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            
10CountVariants  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            
11CountVariants  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            
12
13##:GATKReport.v0.1 SimpleMetricsByAC.metrics : TiTv by allele count
14SimpleMetricsByAC.metrics  CompRod  EvalRod  JexlExpression  Novelty  row  AC  nTi  nTv  n  TiTv
15SimpleMetricsByAC.metrics  dbsnp    eval     none            all      ac0  0   0    0    0  0.0 
16SimpleMetricsByAC.metrics  dbsnp    eval     none            all      ac1  1   0    0    0  0.0 
17SimpleMetricsByAC.metrics  dbsnp    eval     none            all      ac2  2   0    0    0  0.0 
18SimpleMetricsByAC.metrics  dbsnp    eval     none            known    ac0  0   0    0    0  0.0 
19SimpleMetricsByAC.metrics  dbsnp    eval     none            known    ac1  1   0    0    0  0.0 
20SimpleMetricsByAC.metrics  dbsnp    eval     none            known    ac2  2   0    0    0  0.0 
21SimpleMetricsByAC.metrics  dbsnp    eval     none            novel    ac0  0   0    0    0  0.0 
22SimpleMetricsByAC.metrics  dbsnp    eval     none            novel    ac1  1   0    0    0  0.0 
23SimpleMetricsByAC.metrics  dbsnp    eval     none            novel    ac2  2   0    0    0  0.0 
24
25##:GATKReport.v0.1 TiTvVariantEvaluator : Ti/Tv Variant Evaluator
26TiTvVariantEvaluator  CompRod  EvalRod  JexlExpression  Novelty  nTi  nTv  tiTvRatio  nTiInComp  nTvInComp  TiTvRatioStandard  nTiDerived  nTvDerived  tiTvDerivedRatio
27TiTvVariantEvaluator  dbsnp    eval     none            all      0    0    0.00000000  0          0          0.00000000         0           0           0.00000000      
28TiTvVariantEvaluator  dbsnp    eval     none            known    0    0    0.00000000  0          0          0.00000000         0           0           0.00000000      
29TiTvVariantEvaluator  dbsnp    eval     none            novel    0    0    0.00000000  0          0          0.00000000         0           0           0.00000000      
30
31##:GATKReport.v0.1 ValidationReport : Assess site accuracy and sensitivity of callset against follow-up validation assay
32ValidationReport  CompRod  EvalRod  JexlExpression  Novelty  nComp  TP  FP  FN  TN  sensitivity  specificity  PPV  FDR  CompMonoEvalNoCall  CompMonoEvalFiltered  CompMonoEvalMono  CompMonoEvalPoly  CompPolyEvalNoCall  CompPolyEvalFiltered  CompPolyEvalMono  CompPolyEvalPoly  CompFiltered  nDifferentAlleleSites
33ValidationReport  dbsnp    eval     none            all      0      0   0   0   0   NaN          100.00000000  NaN  NaN  0                   0                     0                 0                 0                   0                     0                 0                 0             0                    
34ValidationReport  dbsnp    eval     none            known    0      0   0   0   0   NaN          100.00000000  NaN  NaN  0                   0                     0                 0                 0                   0                     0                 0                 0             0                    
35ValidationReport  dbsnp    eval     none            novel    0      0   0   0   0   NaN          100.00000000  NaN  NaN  0                   0                     0                 0                 0                   0                     0                 0                 0             0                    
36