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How should QC Flags be interpreted and used? #10

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fgmp opened this issue Apr 26, 2024 · 1 comment
Open

How should QC Flags be interpreted and used? #10

fgmp opened this issue Apr 26, 2024 · 1 comment

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@fgmp
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fgmp commented Apr 26, 2024

Are only recombination events that have the QC flag of PASS worth reporting or investigating closer, and all others to be excluded?

I was wondering if pango-designation recombinants like XBC and XBB have PASS in their QC field in the FullTree. If these widely studied recombinants were not flagged with PASS in the FullTree, does that mean I should not just exclude the other putative recombinants that were not flagged with PASS?

@mrkylesmith
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Hi @fgmp. You should not necessarily exclude the other putative recombinants that were not flagged with PASS, since we see several pango-designated recombinants, like XBB and XBC flagged with the Too_many_mutations_near_INDELs flag. These filtration flags are mostly intended to make aware potential quality issues for recombinant designators, however in-practice the flags may be too stringent.

In case its helpful:

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