Comments (2)
BioWilko
commented on August 28, 2024
That's because without using nanopolish or medaka there is no variant caller in the pipeline therefore no vcf files to merge.
If you do not have access to the fast5 files I suggest you use the command:
artic minion --threads 10 --normalise 200 --medaka --medaka-model <insert medaka model here> --scheme-directory ~/Downloads/Bioinfo/fieldbioinformatics/test-data/primer-schemes --strict --read-file ../CERI-KRISP-K032245_ONT.fastq.gz nCoV-2019/V3 CERI-KRISP-K032245_ONT
ONTs medaka repo explains how to determine your medaka model
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idolawoye
commented on August 28, 2024
Thanks!
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Related Issues (20)
- artic pipeline not installing properly: ModuleNotFoundError: No module named 'importlib.metadata' HOT 1
- Longshot `thread 'main' panicked at 'assertion failed: p <= 0.0'` error: possible to update longshot? HOT 3
- vcf_filter.py filtering parameters and align_trim.py for alternative primer scheme
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- Artic v5 mismatched primer names in bedfile causes "dropped" amplicons HOT 1
- Update medaka version HOT 2
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- Clarify what's meant by 'Suppress variant'
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- Custom bed file with "primer gaps" causes workflow to crash at artic-tools vcf_checker step HOT 1
- Error: bcftools consensus fail with overlapping variants HOT 5
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