Comments (1)
I think that would be really interesting, also to compare the final consensuses.
We then just need to be aware of some slight differences in the processing of the files as described here:
https://artic.readthedocs.io/en/latest/minion/
See "Variant calling"
Note: we use the $SAMPLE.trimmed.rg.sorted.bam alignment for the nanopolish workflow as nanopolish requires some leading sequence to make variant calls; we use the primer sequence for this purpose in order to call variants at the start of amplicons.
With medaka, the $SAMPLE.primertrimmed.rg.sorted.bam
is used instead!
from porecov.
Related Issues (20)
- Only calculate NanoPlot after read filtering step HOT 5
- Add new V5 ARTIC primer BED HOT 5
- Medaka step fails in the -profile fastq_test HOT 3
- summary_report.py fails HOT 7
- publish primersitereport from medaka output
- VarSkipV2b primer does not work as expected HOT 7
- Update Medaka to support R10.4.1 models HOT 14
- Update --help to list up-to-date primer schemes that are supported
- MinKNOW/Guppy update needs new model for R10.4.1 5 kHz HOT 6
- Warning when execution report and timeline already exists HOT 1
- The pipeline fails in artic_ncov_wf_artic_medaka HOT 7
- new pangolin table columns HOT 1
- CovarPlot fails w/ custom BED HOT 5
- Process retry in slurm profile HOT 1
- Publish VCF files HOT 2
- Update medaka to get the latest models HOT 1
- Test Freyja Update function HOT 11
- [Question] CI for Variant Calling HOT 5
- Singularity container execution of pangolin crashes with recent nextflow versions HOT 9
- freyja fails with too few reads
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from porecov.