cizydorczyk

Has this been ported to/implemented in BEAST 2 yet? Just getting started with BEAST 2 and been wondering this myself. Thanks!

My mistake - yes, I meant `--opts "careful"`. I left Shovill contig correction enabled. ``` (snippy-env) -bash-4.2$ snippy --version snippy 4.3.6 (shovill-env) -bash-4.2$ shovill --version shovill 1.0.4 ``` Your explanation...

How would bcftools know what is missing/ambiguous (N) if Snippy does not record such positions in its VCF file in the first place? Aren't such sites purposefully left out (i.e....

I've been wondering the same thing recently but here is what I understand: 1) The filtered fasta file contains only polymorphic sites. It is filtered in that any polymorphic sites...

Hi Megan, No, I never was able to figure this out. I use a workaround nowadays, where if I run Gubbins (instead of ClonalFrameML, which I prefer as it doesn't...

I have had this problem when feeding Gubbins/IQ-Tree pseudo-whole genome alignments from Snippy; I'm not sure what's going on but I also have not given it as much investigation as...

Thank you for your response. I was not able to modify my file prefixes but I modified contig names within each assembly to just a number and it resolved the...

I get the same error. Any fixes? Downloaded via conda, v0.0.18.