Open hoelzer opened 3 months ago
Ah wait, it seems we publish them to 3.Lineages_Clades_Mutations
folder
E.g.
are the final variant calls splitted into pass and fail? (what are the default filter values then?)
Yes, the called variants get split based on min_depth
(DP) and min_depth
(QUAL and GQ):
https://github.com/artic-network/fieldbioinformatics/blob/1.3.0-dev/artic/vcf_filter.py#L54-L79
The default values in poreCov are 20 for min_depth
and ${params.min_depth} = 20
for min_depth
- the same as in ARTIC (https://github.com/artic-network/fieldbioinformatics/blob/1.3.0-dev/artic/pipeline.py#L115-L118).
Note, that min_depth
and min_depth
are not available in ARTIC's master branch, only in 1.3.0-dev.
@jonas-fuchs pointed out that VCFs from ARTIC in Galaxy do have allele frequencies. I didn't have time to test it, but it'd be a medaka tools annotate
with additional --dpsp
and this script.
For many downstream analysis it would be nice to also publish the VCF files with the ref/alternate allele and the frequencies.