diff --git a/gnomad/sample_qc/relatedness.py b/gnomad/sample_qc/relatedness.py index 9d771d56..94f776d8 100644 --- a/gnomad/sample_qc/relatedness.py +++ b/gnomad/sample_qc/relatedness.py @@ -1537,7 +1537,7 @@ def default_get_de_novo_expr( """ Get the *de novo* status of a variant based on the proband and parent genotypes. - Confidence thresholds (from Kaitlin Samocha's [*de novo* caller](https://github.com/ksamocha/de_novo_scripts)): + Confidence thresholds (from Kaitlin Samocha's `de novo caller `_): +----------------+--------------+-----------------------+------+------+-------+-----+ | Category | P(*de novo*) | AB | AD | DP | DR | GQ | @@ -1569,7 +1569,7 @@ def default_get_de_novo_expr( .. note:: The “LOW” confidence category differs slightly from the criteria in the - original code (P(*de novo) > 0.05 and AB > 0.2 ), as it is designed to fill + original code (P(*de novo*) > 0.05 and AB > 0.2 ), as it is designed to fill the gap for variants that do not meet the FAIL criteria but would otherwise remain unclassified.