Dan Lu comments

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                                            Dan Lu

augur refine crashes when the root sequence is not included in the build

I'm learning so much through this discussion 😆 I didn't know `--ignore-seqs Wuhan/Hu-1/2019` is in place by default (I see it in our run log). We removed all ref strain...

Keep small number of BA.2 on the tree and not filtered by clock_filter

Updated: We're wrapping up this sprint and will leave this issue to the original assignee ;) Original: We're planning to tackle #852 this sprint. @corneliusroemer do you want us to...

meaning of warning:cant use more than 65535 sites

Good to know! If the sites file has more sites, do the first 65535 sites get used?

meaning of warning:cant use more than 65535 sites

Got it. Thank you!

bcftools csq cannot parse bacterial gff3 files

Thanks for the discussion above! It's very helpful! Please allow me to do a quick summary, and point out that spelling and letter case needs to be exact match: ```...

Enable user-specified path to sidecar JSON files with `fetch`

That's correct. We haven't had any further development on our end.

different results from ska2 0.3.2 and 0.3.6

Let me look through them. Thanks!

duplicate in bam

Very good question. I think below articulates it pretty well (from the CDC covid slack channel). ![image](https://user-images.githubusercontent.com/20667188/127674138-81ddb6f6-6a80-494d-ae38-030ec0652f31.png)

[minor] Better handling of skipping ERCC process

Can implement while migrating to DSL2. Will leave as is if complicated.

exit and print error if kraken2_db not set

Can implement while migrating to DLS2