Chat message

Slack / Private Message Drop, p.546 [SLACK_000760] · slack_pm:msg:05688

Recipients on this medium are inferred from channel membership, not per-message addressing.

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?

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

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
2021-02-24 09:29 Kristian G. Andersen open

If this is from NYC, it's possible they used Illumina's DRAGEN pipeline
2021-02-24 09:29 Kristian G. Andersen open

(I have reached out to them - crickets).
2021-02-24 09:30 Kristian G. Andersen open

shared file(s): image (1).png, Screen Shot 2021-02-24 at 09.30.29.png
2021-02-24 09:34 Andrew Rambaut

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?
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
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
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.
2021-02-24 09:46 Kristian G. Andersen open

B.1.526 with S477N: https://outbreak.info/situation-reports?country=United%20States&division=California[...]1.526&muts=S%3AS477N&selected=New%20York&selectedType=division