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epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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Are homoplasmic site masked when running wf-artic #63

Closed Rohit-Satyam closed 1 year ago

Rohit-Satyam commented 2 years ago

What happened?

I was wondering if the suggestions made by https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473 on sequencing issues with SARS COV2 are accounted for by wf-artic. For instance, when I see data folder for reference assembly, I didn't see any masking of suggested homoplasmic regions. Should I be worried?

Operating System

ubuntu 20.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - Execution Profile

No response

Workflow Version

v0.3.18

Relevant log output

NA
Rohit-Satyam commented 2 years ago

@mattdmem any thoughts on this??

mattdmem commented 2 years ago

Hello @Rohit-Satyam,

wf-artic uses the Network Artic field bioinformatics package which I don’t believe does any masking of potentially homoplasmic sites. An option here is you could easily mask any sites you are concerned about in the consensus sequence before using in any downstream analysis.

There are a few tools out there to do this including this one in the bedtools package

https://bedtools.readthedocs.io/en/latest/content/tools/maskfasta.html

Thanks

Matt