Comments (2)
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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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
- Error with medaka consensus HOT 1
- Unable to install artic on mac
- artic_vcf_merge Fails HOT 2
- What is the default mindepth ? HOT 4
- pipeline has stopped working...! HOT 5
- Conda recipe for 1.2.3 not working HOT 8
- no version information available (required by samtools) HOT 5
- Overlapping variants in fail.vcf and pass.vcf cause preconsensus to be masked and thus bcftools complains when applying the "pass" variant HOT 2
- Artic v5 mismatched primer names in bedfile causes "dropped" amplicons HOT 1
- Update medaka version HOT 2
- KeyError: 'SupportFraction' when running margin_cons.py
- Clarify what's meant by 'Suppress variant'
- Conda environment set up HOT 3
- 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
- htslib =1.17 dependency PLEASE UPDATE HOT 1
- PyVCF assigns a QUAL value of '.' instead of zero
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