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cov-lineages / scorpio

serious constellations of reoccurring phylogenetically-independent origin
GNU General Public License v3.0
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Allow for a rule with more flexibility for indels #29

Closed rmcolq closed 2 years ago

rmcolq commented 3 years ago

For sequences previously designated B.1.1.7 but not passing the scorpio threshold, ref calls were more often in deletions. Would be good to be able to update the definitions to have more flexibility specifically in those cases.

rmcolq commented 3 years ago

E.g. add a max_ref_snp threshold

AngieHinrichs commented 3 years ago

Yes, sadly far too many SARS-CoV-2 genomes have been produced by bioinformatics pipelines that don't detect deletions reliably (not to mention insertions). Good idea to be more lenient on indels.