Closed Shaokang123 closed 3 years ago
May I ask if any one can help answer the question?
At a glance, it looks like the following files will need editing
margin_cons.py
make_depth_mask.py
vcf_filter.py
Sorry for the delay in getting back to you @Shaokang123 - I don't normally monitor this repo and the pipeline dev happens over at artic pipeline.
@bede is right - there is no global pipeline parameter for adjusting minimum read depth per reference base. I'm not sure of the reason to this but I guess it's because we mask out both low coverage bases with N, as well as using coverage during the variant filtering, so having one variable controlling these is a little misleading.
To decrease minimum read depth required per base, you need to adjust the artic_make_depth_mask
command in the minion.py
script - just add --depth 15
. If you want to also change the minimum read depth for variant filtering, you will need to adjust what is happening in vcf_filter.py
.
I think it would be useful to adjust the minimum read depth for the former case here, I'll make a PR to the pipeline repo. Hope this helps, let me know if it doesn't!
I would be keen to see this as a configurable parameter to artic minion. However I would suggest people don't go lower than 20x! Partiularly as nanopolish will not call anything below 20x.
Great. Many thanks to all of you! Appreciate the help. @bede @will-rowe @nickloman
Has there been any movement towards making min depth a configurable parameter to artic minion --medaka? Given all of the recent conversations in the public health community about the effects of minimum coverage depth for variant and consensus calling for SAR-CoV-2, it would be great if there was a more user friendly way to test how changes to workflow parameters (min depth in particular) influences our QC metrics and outputs from artic.
From the documentation, any position that is not covered by at least 20 reads are marked as low coverage and changed to "N". If I want to tweak this parameter, say lower it to 15, which file and line I shall change for artic? Thank you for any help.