How does PHEnix handle plasmids?

Question

How does PHEnix handle plasmids?

Opened this issue 4 years ago · 2 comments

flashton2003 commented 4 years ago

Hello,

I'm using PHEnix for an organism where the reference genome has plasmids.

I want to leave the plasmids in for the mapping and snp calling so that plasmid reads don't map to the chromosome, potentially causing artefacts.

But then, the plasmids should be removed before the phylogeny is constructed.

What is the behaviour of vcf2fasta? Will it output a consensus fasta of the chromosome plus the plasmid?

Thanks!

Phil

Answer 1 · 2020-10-02T14:29:42.000Z

Phil!

I am not entirely sure. Sorry. I haven't used it in a while. Coronaviruses don't have plasmids.

You'd have to experiment. Maybe remove all the lines of mapping to the plasmid from the vcf (or even the sam file) manually before continuing to make the alignment.

Ulf

Answer 2 · 2020-10-02T15:02:33.000Z

Haha, ok, no worries. Thanks Ulf!

…

On Fri, 2 Oct 2020 at 16:29, ulfschaefer ***@***.***> wrote: Phil! I am not entirely sure. Sorry. I haven't used it in a while. Coronaviruses don't have plasmids. You'd have to experiment. Maybe remove all the lines of mapping to the plasmid from the vcf (or even the sam file) manually before continuing to make the alignment. Ulf — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#46 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAT6FEVTVARNPHMDLTB5VLDSIXPWLANCNFSM4SBX7IRA> .