XAC

[szhan]

XAC is a two-breakpoint recombinant as per the pango-designation issues and RecombinHunt-GISAID, but it is a simple recombinant as per sc2ts.

method	pango_parents	breakpoint_intervals
pango-designation	BA.2* + BA.1* + BA.2*	25812-26060; 27384-29510
RecombinHunt-GISAID	BA.2.3 + BA.1.1.16 + BA.2.3	25818-25819; 27381-27382
sc2ts	BA.2 + BA.1.17.2	24504-26060

cov-lineages/pango-designation#590
ktmeaton/ncov-recombinant#124

[hyanwong]

Actually, it's part of the group in #339 in sc2ts

[szhan]

Yes, but this issue is specifically about why XAC is picked up as a simple recombinant by sc2ts rather than a 2-breakpoint recombinant as per pango-designation issues. We could close this if unneeded or confusing?

[jeromekelleher]

Let's keep this open as it's an interesting example. There's a fair bit of tree building going on immediately ancestral to xac, so maybe what happened is that sc2ts is filling in some unsampled gaps that other recombination detection methods cannot.

[szhan]

Just revisiting this. It looks like the second breakpoint relies on evidence of a large deletion (inherited from BA.2*) to the right of 29510 (del29734-29759).

[szhan]

I think this is another case which is detected as a non-recombinant by sc2ts because a deletion is treated as missing data.