will-rowe
commented
3 years ago Hi @tdalpert. Thanks for getting in touch!
As you've pointed out, you can't currently adjust that value via the artic CLI. Please feel free to make a feature request over at the artic pipeline repo
Alternatively, you could try:
- clone or fork the the artic pipeline repo
- update the code to what you want
- follow the installation instructions from the pipeline repo, which has a conda env with just the pipeline dependencies (instead of the env in this repo, which includes the whole pipeline via conda)
Another thing which might work for you is the medaka workflow, which also has a threshold for secondary calls but this is set much lower (0.04) by default. We've not really played with this threshold though so can't advise, though you will probably have to look at parsing the VCFs yourself.
I am working with wastewater samples and would like to identify lower frequency variants, but the code which calls the nanopolish variant command is in the -artic=1.1.3 dependency of the environment and I'm not sure how to fork or edit that myself. Is this possible? I found the line (170) in minion.py in fieldbioinformatics repository (the -m flag is what I would like to change), but not sure if that's compatible or up to date with the ncov2019 repository. Thanks!