Table 1:
Contingency table describing the GA4GH definitions of true positive (TP), false positive (FP), false negative (FN), allele mismatch (FP.AL), genotype mismatch (FP.GT), and unknown (UNK). Matches counted as FP.GT and FP.AL are additionally counted as both FP and FN, since our tool’s default matching stringency requires genotypes to match. Query variants outside the Truth bed file are counted as UNK.
| Truth | ||||||
|---|---|---|---|---|---|---|
| Genotype | ref/ref | ref/var1 | var1/var2 | var1/var1 | Outside bed |
|
| Query | ref/ref | - | FN | FN | FN | - |
| ref/var1 | FP | TP | FP.GT | FP.GT | UNK | |
| ref/var2 | - | FP.AL | FP.GT | FP.AL | - | |
| ref/var3 | - | - | FP.AL | - | - | |
| var1/var2 | FP | FP.GT | TP | FP.GT | UNK | |
| var1/var3 | - | - | FP.GT | - | - | |
| var2/var3 | - | FP.AL | FP.GT | FP.AL | - | |
| var3/var4 | - | - | FP.AL | - | - | |
| var1/var1 | FP | FP.GT | FP.GT | TP | UNK | |
| var2/var2 | - | FP.AL | FP.GT | FP.AL | - | |
| var3/var3 | - | - | FP.AL | - | - | |