Comments (2)
jvolkening
commented on August 28, 2024
1
Okay, thanks for confirming. I'll put together a PR if I have some free time but it's not a priority (probably not for you either).
from fieldbioinformatics.
will-rowe
commented on August 28, 2024
Hi @jvolkening - yes that's exactly what it's doing. It's not ideal; I wrote it to quickly spot amplicon drop out rather than report depths from the depth file. It should really ignore the adjacent amplicon from the other readgroup, as you point out.
Hopefully I'll get around to improving this soon (although PR would be welcome if you fancy it). Cheers.
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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