GT-precision calculation about truvari HOT 3 CLOSED

Formulas for the metrics and gt_matrix table structure are described in the wiki. Your table shows

If you define TP as compGT == baseGT - you get 4305 + 1667 = 5972.
The difficulty for applying the metrics to FN/FP genotypes is they're symmetrical since every baseGT has a compGT to compare to. But you could say FN/FP counts are 3178 + 4 = 3182. Plugging these totals in gives 0.652392397 precision and recall.

Because of this symmetrical FN/FP, Truvari reports the summary metric as gt_concordance:
"TP-comp_TP-gt" / ("TP-comp_TP-gt"+ "TP-comp_FP-gt") Which is also 0.652392397

from truvari.

Precision = TP / (TP + FP)
"Can we understand this as GT-precision = 0.652392397?"
Recall = TP / (TP + FN)
How to calculate GT-Fn？
How to calculate GT-recall?

from truvari.

Please see previous post. Or just use gt_concrdance.

from truvari.