search

Clinical-Genomics / chanjo

Chanjo provides a better way to analyze coverage data in clinical sequencing.
https://clinical-genomics.github.io/chanjo/
MIT License
49 stars 12 forks source link

Time to update transcripts #225

Open 47KW opened 3 years ago

47KW commented 3 years ago

Får inte upp coverage (alternaivt inte heller calls) för CFAP43 https://scout.scilifelab.se/cust002/F0037468 namnändring har skett av genen påpekas

dnil commented 3 years ago

Thank you! Not sure yet if this is a bug or a local issue; for one chanjo may not yet be in sync with scout after this afternoons update, but the fact that you can't see variants in the gene gives off a feeling of an issue somewhere else as well..

northwestwitch commented 3 years ago

Checked quickly in chanjo database. Doesn't look like that there is a CFAP43 gene

image

northwestwitch commented 3 years ago

I don't find it even by transcript:

image

dnil commented 3 years ago

See if it has WDR96 still perhaps.. But that should have been changed already last year? The highest ranking variant in the vcf was RankScore=2, and most far on the negative side, so no issue with loading in Scout at least. I think this is an isolated chanjo update issue then.

northwestwitch commented 3 years ago

See if it has WDR96 still perhaps..

Nope:

image

dnil commented 3 years ago

Time to export genes and reload chanjo perhaps? After checking there is a good backup perhaps? 😬

northwestwitch commented 3 years ago

Yes, the issue should be moved there I think

moonso commented 3 years ago

Yes I agree that it is really time for Chanjo, it will require some efforts though. I suggest to make a project suggestion here https://github.com/Clinical-Genomics/project-planning/issues/ so we can prioritise along with all the other stuff

northwestwitch commented 3 years ago

I've created a new associated project to this in project-planning. Who should be in charge of it?