Scorpio overriding UShER calls for XD recombinants

cov-lineages / scorpio

serious constellations of reoccurring phylogenetically-independent origin

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Scorpio overriding UShER calls for XD recombinants #45

Open SVN-PhD opened 2 years ago

SVN-PhD commented 2 years ago

Running these tools in default UShER mode.

pangolin v4.0.6
pangolin-data v1.8
constellations v0.1.9
scorpio v0.3.17

Many sequences that should be XD (labelled clade GKA on GISAID) are getting called as AY.4. Looking at the notes, it seems scorpio is overriding the UShER calls and misclassifying them instead. Check the lineage report attached along with accessions of sequences that are miscalled. Thanks!!

lineage_report_USHER.csv

corneliusroemer commented 2 years ago

Has this been resolved @aineniamh?