-
Notifications
You must be signed in to change notification settings - Fork 107
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Non-SCV2 amplicon run returns consensus genomes with no low-coverage masking #420
Comments
Hi @ddomman ! We are using viralrecon with amplicon RSV data too and it masks perfectly the consensus using ivar as variant caller and bcftools as consensus genome generator. We would need to replicate you specific analysis. Would you mind to send us the files you used and the command to run viralrecon? |
Halo @svarona could you please inform me of the specific commands you input to conduct the analysis for RSV? I've been attempting it myself but without success. Could you kindly provide the commands used for the Illumina and Nanopore platforms, if possible? |
Hi @chocogangsta. Viralrecon can't run on RSV nanopore data, because it uses ARTIC protocol, which works only for SARS-CoV-2. For Illumina sequencing these are the commands we're using:
|
@ddomman We've seen cases were bcftools won't substitute variants neither mask the consensus genome, rendering a consensus genome exactly the same as the reference genome. Which can be due to non linux new line characters on the reference .fasta used (usually due to its edition on microsoft word). I assume that this one is not your case as you say that it is replacing variants properly. |
I'm having the same issue with the current 2.6.0, sars-cov-2 genomes. |
Description of the bug
Viralrecon has worked perfectly for our SCV2 and some hybrid capture protocols (with the metagenomic side). However, when I ran the pipeline by passing a custom bed file and fasta reference for RSV, the default pipeline produced consensus genomes that have no low coverage mask or Ns. It appears the bcftools consensus pipeline IS substituting the variants but for all low coverage areas, the reference base is given rather than Ns.
Switching over to the iVar consensus option (
--variant_caller ivar
,--consensus_caller ivar
), pipeline produces correct consensus genomes with low coverage areas masked with Ns.Command used and terminal output
No response
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered: