Skip to content
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.

Sign up for GitHub

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

Jump to bottom

ivar trimming of Swift libraries new offset feature #170

Closed
rrdavis77 opened this issue Apr 1, 2021 · 1 comment
Closed

ivar trimming of Swift libraries new offset feature #170

rrdavis77 opened this issue Apr 1, 2021 · 1 comment
Labels
enhancement Improvement for existing functionality
Milestone
2.0

Comments

@rrdavis77
Copy link

Came across these improvements for ivar in the IDseq github:

chanzuckerberg/idseq-workflows@d922823

andersen-lab/ivar#88

When processing swift libraries polymerases can add additional bases causing issues with trimming. I guess this happens for swift libraries only?
@drpatelh drpatelh added the enhancement Improvement for existing functionality label Apr 27, 2021
@drpatelh drpatelh added this to the 2.0 milestone Apr 27, 2021
@drpatelh drpatelh mentioned this issue Apr 27, 2021
Merged
@drpatelh
Copy link
Member

Added a new parameter called --ivar_trim_offset to be able to customise this behaviour. As suggested in the issues linked to above if you are using the SWIFT/SNAP protocol then you will need to set --ivar_trim_offset 5 when running the pipeline.

The pipeline will also now attempt to auto-detect whether you are using the SWIFT/SNAP protocol based on the assumption that you have used covid19genome in the name field of the primer BED file. This name is used in the original SWIFT master file containing the primer co-ordinates.

image

drpatelh added a commit that referenced this issue Apr 28, 2021
@drpatelh
Add warning for #170
ece8c56
stenglein-lab added a commit to stenglein-lab/viral_variant_caller that referenced this issue Jul 26, 2022
@stenglein-lab
Added two parameters to increase stringency of variant calling:
701d8c2 
1. Changed clipping penalty parameter in bwa mem from 5 to 1.  This favors more soft-trimming at the ends of reads.  Since variants at the ends of reads are less reliable, this reduces false-positive variant calling.
2. Expanded ivar trim trimming using the -x offset parameter.  This trims extra bases around primer binding sites.  This also makes variant calling more stringent.

See these issues for more information on these settings:

nf-core/viralrecon#170

andersen-lab/ivar#88
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
enhancement Improvement for existing functionality
Projects
None yet
Milestone
2.0
Development

No branches or pull requests
2 participants
@rrdavis77 @drpatelh