nf-core/raredisease MT variants loading

Clinical-Genomics / scout

VCF visualization interface

https://clinical-genomics.github.io/scout

BSD 3-Clause "New" or "Revised" License

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nf-core/raredisease MT variants loading #4672

Closed dnil closed 3 months ago

dnil commented 3 months ago

Describe the bug MT vars from nf-core/raredisease not displaying.

To Reproduce

Load split out MT VCFs scout load case -u scout_load.funkitten.yaml Screenshot 2024-06-10 at 15 07 01 ... 99 MT vars show inserted BUT no MT vars appear when filtering?! Screenshot 2024-06-10 at 15 13 00 Chromosome naming, ranking or load error?

dnil commented 3 months ago

The variants appear to have contig MT so all good, but few with decent rank score...

northwestwitch commented 3 months ago

The variants appear to have contig MT so all good, but few with decent rank score...

Perhaps the counter doesn't update then? But also where are the variants?

dnil commented 3 months ago

They are loaded at least:

And it shouldn't be the scores, we are committed to loading all on CHROM "MT".

dnil commented 3 months ago

False alarm! When unchecking panel, and showing also variants from unaffected individuals only, all is good: Screenshot 2024-06-10 at 15 35 11