search

Clinical-Genomics-Lund / SomaticPanelPipeline

0 stars 2 forks source link

Markgermline rank #34

Closed ViktorHy closed 2 months ago

ViktorHy commented 9 months ago

Added support for more in-depth assigning of GERMLINE to paired samples. This should make it able to have a lot of genes available for germline analysis but still not get overwhelmed by variants. Right now it disqualifies variants with high gnomad frequencies. It tries to include variants with severe conseqences on protein and variants with clinvar annotations.

All three categories are modifiable in a JSON-config as well as defining all GERMLINE genes of interest.

ViktorHy commented 9 months ago

Have not tested tumor-only cases. TODO

ViktorHy commented 2 months ago

I have now tested this for paired solid samples and for one paired parp sample and it generates correct files. Sample tested has been noted in internal document on teams