GWAS with SAIGE - how to proceed

Question

[a_confused_biologist]

Hi all,

I got my hands on some GWAS results analysed with SAIGE by a collegue. I would like to map the results onto genes and pathways. As I am really unfamiliar with this type of data, I would like to ask for your help.

For each variant I have the following columns:

• variant ID
• chromosome
• genome position

• effect allele

• non-effect allele

• effect allele count

• effect allele frequency

• standard error of BETA

• score statistic of effect allele

• p.value

• estimated variance of score statistic with sample relatedness incorporated

• variance of score statistic without sample relatedness incorporated

• effect allele frequency in cases

• effect allele frequency in controls

Any type of help regarding which packages or tools I can use would be much appreciated!

EDIT: Formatting

[Sam]

FUMA might be a good starting point: https://fuma.ctglab.nl/

[a_confused_biologist]

Thank you for your suggestion! Are you aware of alternatives that could be run locally on my computer instead?

[Sam]

MAGMA might be a good start. It isn't too complicated but does require a bit more knowledge on the different file formats and data. Considering what you mentioned in your post, FUMA might be a better choice esp considering that you are only providing a summary statistics, which usually isn't as restrictive as the raw genotype data.