damiansm
damiansm
As ever I am ignorant of the steps before Exomiser. Max - are you talking about the reduction in performance of variant calling when you use single VCFs as you...
Now published as SQUIRLS: https://pubmed.ncbi.nlm.nih.gov/34289339/ Presumably we can now close https://github.com/exomiser/Exomiser/issues/133 and just focus on how to incorporate SQUIRLS into Exomiser analysis. I have successfully generated a tabix score files...
Hi Andrew, We use Jannovar as the library for variant annotation and segregation filtering so we are going to have to delve into what is happening in there. @pnrobinson and...
@visze @julesjacobsen @pnrobinson I combined the 3 prev issues discussing this into one new issue as they are all inter-related and to simplify the discussion!
@julesjacobsen Is this now done? Can see this file is part of the phenotype-build code now
Looks like this may have been done? Lets just test this with a dummy VCF of unit test!
Best to use MANE (+ MANE clinical) for this
@julesjacobsen Yes - this recent work makes this task a lot easier. It could be as easy as trimming the disease2gene table we load into Exomiser based on knowledge from...
I guess GenCC has potentially conflicting classifications for the same OMIM or Orphanet disease ID whereas ClinGen will have a consistent annotation? One option is to just take all Definitive...
Lets decide what if we are going to use the data for first and for what? If we just want to have a definitive only setting then we can just...