Comments (3)
This issue may introduce wrong ref. allele reversions. Because --strict
option is useful to deal with some other bugs, I think it's best to mask these sites (assumed contamination) instead of pad them with ref alleles.
from fieldbioinformatics.
Thanks for the comment. Wondering which other bugs would be introduced by negating the --strict mode.
from fieldbioinformatics.
Thanks for the comment. Wondering which other bugs would be introduced by negating the --strict mode.
I don't remember in details but somethings related to the conflicts between failed and passed vcf that makes bcftools failed.
Maybe this one, I think artic-tools::check_vcf somehow can help overcome the issue?
from fieldbioinformatics.
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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from fieldbioinformatics.