Snp_matrix <- fread("File.raw") Out of Memory

Hail Query & hailctl
1

Hello,
I would like to perform a GWAS and I already have the .map and raw. files with the phenotype file but the raw file weight 4Go ( output ls -l on puhti server -rw-rw---- 1 huguetho huguetho 4004201413 Aug 4 13:10 All_samples_imputed.raw).

I first tried to upload the file under Rstudio but it’s out of memory so then I tried directly on puhti but same and then by a pipeline but I still have error and the GWAS didn’t work. Maybe missing something.
Does anyone can advice me about GWAS on huge data ? How to perform the model and display Manhattan and QQ plot ?

Best

2

Hi @HugHo,

Sorry, but this question doesn’t look like it’s about the Hail software. This forum is specifically for help with Hail, not general computational genomics.

Hail is an excellent option for computing GWAS on huge data; see for instance our tutorial.