How should QC Flags be interpreted and used?

[fgmp]

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]

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:

• For a description of the QC flags please see the About Page
• A few examples of detected trios tagged with a filtration flag by RIVET due to QC issues: Extended Data Fig. 3: Examples of detected trios filtered out due to sequence quality concerns.