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- [ ] MT variants VCF
~MT variants rank model key~
~MT variants rank model file (link on e.g. reference-files)~
We keep the same variant type (SNV on the chromosome MT).
We postpone making a ne…
dnil updated
5 months ago
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### Description of the bug
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /cfs/klemming/home/h/halfdan/nfc_rd/test_full/work/singularity -- Use the…
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To be invoked by cg to create the delivery report, see https://github.com/Clinical-Genomics/cg/pull/3267
Should ideally accept a query like this:
```
query = {
"build" : "GRCh37"
"sam…
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I'm getting the following error loading a case from nf-raredisease into a fresh install of Scout:
```
Traceback (most recent call last):
File "/home/fearnleyl/scout/scout/adapter/mongo/variant…
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### Description of the bug
The vcfs from tomte are not compatible with scout. Scout requires only one alternative per line
This can be fixed by:
```
bcftools norm -m -both input.vcf.gz > outpu…
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Possible alternatives are not compatible with the ones in the documentation.(PED file format: Sex (1=male; 2=female; other=unknown))
https://github.com/nf-core/raredisease/blob/1489b71cc0e15ade7e9…
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### Description of the bug
I'm getting an error when trying to run the pipeline. The test profile works fine, so it's very likely that I'm doing something wrong, but I can't figure it out. I have not…
fa2k updated
5 months ago
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As a clinician or researcher, I want SNVs to be annotated, ranked and compatible with Scout.
# Suggested approach
Multisample/case_id vcfs are annotated, then split after annotation.
#### Annotate …
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**Describe the bug**
Our geneticists asked whether the compound top 20 on the SNV/indel page works as intended.
Here is one example:
![compound_page](https://github.com/user-attachments/asset…
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### Description of the bug
See https://github.com/Clinical-Genomics/scout/issues/4397 and https://github.com/Clinical-Genomics/scout/pull/4577. In particular we identify the DOMAINS field of the INFO…
dnil updated
5 months ago