vignettes/A1_representation.Rmd
A1_representation.RmdDescribe some approaches currently ongoing in Vince Carey’s group to facilitate work with GWAS and GWAS summary statistics.
Bioconductor 3.17 package BiocHail includes facilities that demonstrate how a) we can perform GWAS using Hail within R and b) we can work with 7200+ phenotypes from UKBB, again in the Hail framework.
These activities can be conducted with any CPU but benefit from Spark cluster + hadoop. A basic question is – how many cloud storage providers can be used to interrogate MatrixTables via HTTPS? Currently it seems only GCP dataproc and Google storage can be used for such focused interrogation.
See https://vjcitn.github.io/BiocT2T to see how to work with 3202 variant profiles (only chr17) in the T2T-CHM13 reference build.
This involves a 65 GB MatrixTable. We use egress-free storage provided to VJC by NSF to place the MatrixTable on user’s local drive.