Annotation of VCF in beacon2-ri-tools-v2

[solcos]

Add in documentation or in a pipeline, how to annotate the VCF in order to transform the annotations to the BFF.

Eg.

• General pipeline
• Rules for the annotation
• Other possibilities

[costero-e]

Create templates to add a custom pipeline to beacon2-ri-tools-v2

[albodrug]

Hello.

Is it currently possible to convert annotations in the vcf file with tools-v2?

[costero-e]

Hi @albodrug,

yes but now the options are limited. All the annotations we are allowing can be found in the https://github.com/EGA-archive/beacon2-ri-tools-v2/blob/main/pipelines/default/templates/default.json file, which are frequencyInPopulations and clinicalInterpretations. For reading your own annotations, please add how you are annotating these entities in your .vcf and the app will read them properly, e.g. having your clinicalRelevance attached to CLINVAR_CLNSIG keyword, you have to fill in caseLevelData|clinicalInterpretations|clinicalRelevance as CLINVAR_CLNSIG. However, we are working on adding more annotations, improving other reads as alleleFrequency and on quality checks for the annotations. If you'd like to add an annotation that can't be read as how the tool is now, please let us know here in issues and we will implement it to have it working for you.

Best,

Oriol