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!!
Running these tools in default UShER mode.
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