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Home Page: https://chorscroft.github.io/MR-and-selection/
Documents and code for the MR and selection project
Home Page: https://chorscroft.github.io/MR-and-selection/
ieu-b-109
bbj-a-1
Use this pipeline to re-run number of children GWAS:
https://github.com/MRCIEU/BiobankPhenotypes/wiki
This will allow the use of raw counts in the GWAS, might make interpretation clearer as it will resemble the simulations
Also - stratify by decile
So the objective here is to take the GWAS for males and GWAS for females, and create a new one which has the same number of SNPs but a single combined effect for each SNP. In doing so we can also test each SNP whether they have different effects in males and females using a heterogeneity test statistic.
You should be able to download them from here:
https://gwas.mrcieu.ac.uk/datasets/ukb-b-1209/
https://gwas.mrcieu.ac.uk/datasets/ukb-b-2227/
Extract from gwas-vcf format to plain text format e.g.
https://github.com/MRCIEU/gwas2vcf/blob/master/README.md#export-to-nhgri-ebi-gwas-catalog-format
Use a tool like METAL to meta-analyse the
https://genome.sph.umich.edu/wiki/METAL_Documentation
What you do is create a configuration text file that specifies the files, the columns in the files, and what analysis to run. Then you pass that file to the METAL binary
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