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cov-lineages / pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages.
GNU General Public License v3.0
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Conflicting results in historical samples (unassigned). Constellation_version: v0.1.10 #456

Closed elrubio89 closed 2 years ago

elrubio89 commented 2 years ago

Hello, We have identified samples with Unassigend linages when updating the constellation version to v0.1.10. These samples present coverage >0.8. The scorpio call assigns them as: Omicron (Unassigned) or Probable Omicron (Unassigned).

aineniamh commented 2 years ago

Hi @elrubio89, in the latest version of pangolin v4.1, we no longer overwrite usher assignments if they don't agree with scorpio calls. Scorpio is still run and the output is reported, but will now only overwrite in pangoLEARN mode to eliminate false positives. Hope that helps resolve your issue.