Max

I'm still working on the jannovar pedigree filter and I will extend it to large pedigrees. But this does not cover: - incomplete penetrance - Analyzing patients from different (searching...

Hi, CADD 1.6 integrates now spliceAI and MMSplice. See the release notes: https://cadd.gs.washington.edu/static/ReleaseNotes_CADD_v1.6.pdf Of course a general score is not able to beat specific scores in predicting splice-predictions but the...

With single vcf we will not have a combined calling. This will reduce the performace! Of course, uploading them separately will make it more easier for lot of users. But...

@damiansm no. I mean 3 variant calling on its own is different to multiple vcf calling on the complete trio at the same time. If separate variant calls are made...

I have the same issue. I think in the conda files (`requirements.txt`) the `phantompeakqualtools` are missing. `r-spp` alone does not provide the script `run_spp.R`

I can give you an example. Have a look at this screenshot.  Imagine a mutation between the two non-coding exons, e.g. `chr19:45926964T>C`. A possible HGVS nomenclature will be `ERCC1:NM_001166049.1:c.-8+75A>G:p.(=)`...

Thank you Karen. We will use the terms in [Jannovar](http://charite.github.io/jannovar/), a tool for variant annotation.

Maybe for annotating variants without prioritization jannovar might be a better choice. Jannovar can annotate several other sources like dbNSFP. ReMM directly is not implemented yet but, if needed, I...

Thank you for the hint. I think we can integrate something like a java version check but I think we will do this only in the command line interface

Year I am aware of that. This will need a complete refactoring of the actual ineritance-mode checker. Right now I have no time for this. But maybe in the future