Conflicting results between parent_clade and parent_lineage

[ktmeaton]

Conflict has been observed between the populations reported between parent_clade and parent_lineage. Example:

• parent_clade: Omicron/BA.4/22A,Omicron/BA.2.12/22C
• parent_lineage: BA.5.2.1*,BA.2.12.1*
• parent_lineage_confidence: 0.28,0.688

Note that the first parent is contested, as the clade is reported to be BA.4, while the most likely lineage is BA.5.2.1*. This conflict is also seen in the first parent's confidence, which is low at 0.28.

To draw attention to this, I could create a new field called parent_conflict. If a parent_lineage is not a descendant of the corresponding parent_lineage, this field could be set to true.

At first, this will just be a field for exploratory purposes. But if it appears to help with identifying false positives, this could be a default filter to excluded samples with parent conflict.