Genome-Wide Association Study (GWAS)¶
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Google BigQuery can be used to perform a GWAS. Here are several examples:
- Chi-squared tests on 1,000 Genomes dataset with members of EAS super population as case and control all other populations:
- Two-proportion Z test on 1,000 Genomes dataset with members of EAS super population as case and control all other populations:
- Chi-squared test on 1,000 Genomes dataset with case and control determined by clustering from a PCA:
To run this on your own data:
- First, load your data into Google Genomics and export your variants to BigQuery. See Load Genomic Variants for more detail as to how to do this.
- For data with non-variant segments (e.g, gVCF or Complete Genomics data), reshape the data into multi-sample variants format via Multi-Sample Variants Format