This video describes a common framework for designing portable federated pipelines. The joint cohort genotyping pipeline is provided as a specific implementation example. The ability of the pipeline to run in different environments, accessing the data via different protocols, and applying the appropriate normalisations is demonstrated.
Read MoreThis month’s blog was written by Dylan Spalding (EMBL-EBI), Coordinator of the European Genome-phenome Archive and co-WPL of CINECA WP4 - Federated Joint Cohort Analysis. This blog is the first in our new series, presenting an overview of GA4GH standards being developed and implemented by CINECA.
Read MoreAuthors - Álvaro González (CSC), Shubham Kapoor (CSC), Kirill Tsukanov (EMBL-EBI)
The federated analysis platform defined by this task aims to provide technological solutions for three exemplar use cases: Federated joint cohort genotyping; Polygenic Risk Scores (PRS) workflow across two similar ethnic background sample sets; Federated QTL analysis for molecular phenotypes. In this deliverable, we gathered the technical requirements based on these use case descriptions and wrote a short design document which explains the requirements and lists the different options for a solution.
Three distinct frameworks were considered to address the requirements from the use-cases. The chosen framework supports different computing environments, which is a requirement for true federated analysis. The framework also supports extending compatibility with GA4GH standards, such as WES, htsget, and AAI / Passports. Plans to extend this proposed solution beyond these initial sites will be carried out after the initial phase of validation.
https://doi.org/10.5281/zenodo.4609356
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