COVID-19 Records

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Slack / Private Message Drop, p.546 [SLACK_000760] · slack_pm:msg:05687

Page text: p.546 · original PDF

Date
2021-02-24 09:30
Type
chat message · slack
recipient
Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker
Kristian G. Andersen

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shared file(s): image (1).png, Screen Shot 2021-02-24 at 09.30.29.png

In context

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  1. 2021-02-24 09:29 Robert F. Garry open
    HMMMM - that is interesting.
  2. 2021-02-24 09:29 Kristian G. Andersen open
    Oh... We have identified a MAJOR issue with Illumina's consensus caller - it's calling reference calls if there are _any_ mismatching reads at a variant site. That might be why
  3. 2021-02-24 09:29 Kristian G. Andersen open
    If this is from NYC, it's possible they used Illumina's DRAGEN pipeline
  4. 2021-02-24 09:29 Kristian G. Andersen open
    (I have reached out to them - crickets).
  5. 2021-02-24 09:30 Kristian G. Andersen
    shared file(s): image (1).png, Screen Shot 2021-02-24 at 09.30.29.png
  6. 2021-02-24 09:34 Andrew Rambaut open
    Interesting - we have seen quite a lot of 'reversions' in some of the VOCs. Who would be using this consensus caller? Is there a way to find out?
  7. 2021-02-24 09:34 Kristian G. Andersen open
    Preprint on the NYC sequences - pretty interesting. https://www.biorxiv.org/content/10.1101/2021.02.14.431043v2.full.pdf
  8. 2021-02-24 09:34 Kristian G. Andersen open
    I'm worried A LOT of people are using the Illumina pipeline - and there's no way to find out in most cases
  9. 2021-02-24 09:35 Kristian G. Andersen open
    Any lab that hasn't previously been involved in virus sequencing and isn't as comfortable with command line tools would likely use this caller. It's a big big problem.

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