In the process of implementing issue #111 , move the SO ranking out of the dark depths of modify_scout_vcf.pl and banish it to the same (as of now hypothetical) repo as our rank models.
The ranking could then—like the rank models—be included as a path in the pipeline config (where it belongs) and passed to the modify_vcf_scout.pl script.
Keeping it as its own file makes it easier to version it, which I think is a worthwhile thing to do if we ever want to keep track of the reasons behind any deviations from the VEP ranking.
See discussion here: https://github.com/Clinical-Genomics/scout/issues/4417#issuecomment-1943875398
This issue concerns the following ranking:
https://github.com/Clinical-Genomics-Lund/nextflow_wgs/blob/a7f1317301391710ae68310cf9a435c6a29bdf59/bin/modify_vcf_scout.pl#L30-L68
In the process of implementing issue #111 , move the SO ranking out of the dark depths of
modify_scout_vcf.pland banish it to the same (as of now hypothetical) repo as our rank models.The ranking could then—like the rank models—be included as a path in the pipeline config (where it belongs) and passed to the
modify_vcf_scout.plscript.Keeping it as its own file makes it easier to version it, which I think is a worthwhile thing to do if we ever want to keep track of the reasons behind any deviations from the VEP ranking.