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Non-recombinant: XP #345

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szhan opened this issue Feb 25, 2025 · 1 comment

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szhan commented Feb 25, 2025 •

edited by jeromekelleher

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cov-lineages/pango-designation#481

Often cannot be detected by sc2rf and is handled as an edge case ktmeaton/ncov-recombinant#136

XP has been mentioned in many issues (e.g., #285).

In brief, XP is not picked up as a recombinant by sc2ts, because we are missing a characteristic deletion.

Also, it was not detected as a recombinant by RecombinHunt-GISAID, but it was by RecombinHunt-Nextstrain.

szhan mentioned this issue

Full list of non-recombinants as per sc2ts #344

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szhan changed the title XP Non-recombinant: XP

Owner

jeromekelleher commented Feb 25, 2025

We should rerun the match for XP samples with deletions-as-missing=False to see if we call it a recombinant then. I'll do this at some point.

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