Comments (6)
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!
from artic-ncov2019.
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.
from artic-ncov2019.
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 artic-ncov2019.
May I ask if any one can help answer the question?
from artic-ncov2019.
At a glance, it looks like the following files will need editing
margin_cons.py
make_depth_mask.py
vcf_filter.py
from artic-ncov2019.
Great. Many thanks to all of you! Appreciate the help. @bede @will-rowe @nickloman
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Related Issues (20)
- Conda environment dependency issues with new versions of Medaka
- nanopolish index -s failure / prime scheme download failure
- Error in Artic filter
- PR to add a new primer scheme? HOT 2
- artic_vcf_filter fails
- Installation via conda (different ways) failed HOT 1
- Artic enviroment does not install after 7 days HOT 2
- V4.1 scheme and primer BED file HOT 3
- Medaka failed: Command failed:longshot -P 0 -F -A --no_haps HOT 1
- multiple references in V4.1 refereces.fasta -> "FASTA has more than one sequence"
- Nanopolish error HOT 3
- Changing Minimum Sequencing Depth Parameter in artic-ncov2019 HOT 1
- Installing ARTIC stuck at Solving environment HOT 1
- artic assembly - Command failed:muscle -in & -out HOT 2
- Midnight primers scheme
- Update to V4/V4.1 under primer-schemes but not artic-ncov2019
- Error running artic minion
- align_trim ValueError: min() arg is an empty sequence (artic 1.2.1) HOT 1
- Error running nanopolish
- Help with vcf_merge HOT 1
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