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ukhsa-collaboration / PHEnix

Public Health England SNP calling pipeline.
http://phenix.readthedocs.io/en/latest/
GNU General Public License v3.0
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How does PHEnix handle plasmids? #46

Open flashton2003 opened 3 years ago

flashton2003 commented 3 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

ulfschaefer commented 3 years ago

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

flashton2003 commented 3 years ago

Haha, ok, no worries.

Thanks Ulf!

On Fri, 2 Oct 2020 at 16:29, ulfschaefer notifications@github.com 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

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