Chat message

Slack / Private Message Drop, p.545 [SLACK_000759] · slack_pm:msg:05684

Date: 2021-02-24 09:29
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen

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

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

In context

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

2021-02-24 09:22 Kristian G. Andersen open

Yeah, B.1.526 with eek is definitely rising in New York. This might be real. https://outbreak.info/situation-reports?country=United%20States&division=California[...]1.526&muts=S%3 AE484K&selected=New%20York&selectedType=division
2021-02-24 09:27 Robert F. Garry open

Speaking of the WSJ - they just requested an interview to discuss our Virological post.
2021-02-24 09:27 Andrew Rambaut open

It is weird the V701A reverting in the S477N lineage - maybe the tree is wrong
2021-02-24 09:29 Robert F. Garry open

HMMMM - that is interesting.
2021-02-24 09:29 Kristian G. Andersen

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 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?

Full conversation →