This repo has some misc examples and helper scripts dealing with genotype data and GWAS.
- gwas101.ipynb downloads a synthetic dataset (
chr21.[bed/bim/fam]) with genotypes for N=10.000 subjects and M=150.000 variants on chr21, and uses this data to illustrate GWAS and polygenic risk scoring. To synthesize the output phenotype the tool uses simu_linux tools, which is not available for MAC or Windows (if you have time to fix this please let me know!).gwas101.ipynbalso examplifiesread_bed,write_bed,nancorrfunctions from gwas_tools.py - some basic helper functions equivalent to MATLAB scripts (matlab/PlinkRead_binary2.m,matlab/nancorr.m) - sumstats/clean_scz2_gwas.ipynb and sumstats/manipulate_gwas_sumstats.ipynb give few examples of dealing with external summary statistics.
- sumstats/sumstats/daner_PGC_SCZ52_0513a.hq2.yaml gives an example of a .yaml file needed for https://github.com/BioPsyk/cleansumstats pipeline.
- misc codes is not something you want to use, just ignore this!
Another useful resource is https://github.com/ofrei/opensnp, see its README file for more info.