Summary statistics IO and methods

The MRC IEU at Bristol has a specification for storing GWAS summary statistics in a VCF file.

While I certainly have mixed feelings about using VCF files as a container format, they have done the hard work of providing tens of thousands of GWAS summary statistics VCFs at the OpenGWAS project.

There are more details in

• The MRC IEU OpenGWAS data infrastructure (2020)
• The variant call format provides efficient and robust storage of GWAS summary statistics (2021)

It would be great to figure out how to map the data in these GWAS VCF files to the sgkit data model and to write some methods on top of them.

[hammer]

So, looking at a few example GWAS-VCF files, they’re just putting per-variant sumstats into the SAMPLE fields. It appears some files use the INFO field for variant-specific metadata like minor allele frequency that we might want to pick up as well, but otherwise, I don’t think parsing is going to be too challenging.

The hard part for us is figuring out if we want to define a blessed data model for sumstats and start adding operations that operate upon it.

[hammer]

New standard for summary statistics https://ebispot.github.io/gwas-blog/new-standard-for-gwas-summary-statistics