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GWAS with SAIGE - how to proceed

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

saige snp gwas
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updated by Sam Sam • written by a_confused_biologist • a_confused_biologist

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

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written by a_confused_biologist • a_confused_biologist

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.

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written by Sam Sam

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