Metrics
Category Metrics
Overview
Class that holds summary metrics about Genotype Concordance @author George GrantThis table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| VARIANT_TYPE | The type of the event (i.e. either SNP or INDEL) |
| TRUTH_SAMPLE | The name of the 'truth' sample |
| CALL_SAMPLE | The name of the 'call' sample |
| HET_SENSITIVITY | The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN)) |
| HET_PPV | The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP)) |
| HET_SPECIFICITY | The specificity for all heterozygous variants cannot be calculated |
| HOMVAR_SENSITIVITY | The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN)) |
| HOMVAR_PPV | The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP)) |
| HOMVAR_SPECIFICITY | The specificity for all homozygous variants cannot be calculated. |
| VAR_SENSITIVITY | The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN)) |
| VAR_PPV | The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP)) |
| VAR_SPECIFICITY | The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN)) |
| GENOTYPE_CONCORDANCE | The genotype concordance for all possible states. Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made |
| NON_REF_GENOTYPE_CONCORDANCE | The non-ref genotype concordance, ie for all var states only. Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made |
GATK version 4.5.0.0 built at Tue, 9 Jan 2024 14:37:17 -0500.
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