Replace genome_ref file with Bioconductor data

[bschilder]

Downloading the genome_ref file is one of the slower steps.

input_url <- "https://ctg.cncr.nl/software/MAGMA/ref_data/g1000_eur.zip"

Would be best if we could switch to using a Bioconductor package that has the same info, and then save that to disk so MAGMA can access it.

e.g.
https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.1000genomes.hs37d5.html

[bschilder]

Currently, we only use the European subset of 1KG. We should definitely expand to the other sub-populations MAGMA makes available as well:

https://ctg.cncr.nl/software/MAGMA/ref_data

[bschilder]

After exploring BSgenome.Hsapiens.1000genomes.hs37d5 it seems this is just a single genome ref (not the individual-level genotype data from 1kg). It's also only phase 2 data.

After some additional searching, I can't seem to do any package that contains the data we're looking for. So for now, sticking with the MAGMA data.