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Scorpio overriding UShER calls for XD recombinants #45

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SVN-PhD opened this issue May 2, 2022 · 1 comment
Open

Scorpio overriding UShER calls for XD recombinants #45

SVN-PhD opened this issue May 2, 2022 · 1 comment
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@SVN-PhD
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SVN-PhD commented May 2, 2022

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 corneliusroemer transferred this issue from cov-lineages/pango-designation Aug 21, 2022
@corneliusroemer
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Has this been resolved @aineniamh?

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@SVN-PhD @corneliusroemer