how to generate covariance matrices for UKB data?
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Entering edit mode
4.5 years ago
anamaria ▴ 220

Hello,

I plan to run MetaXcan https://github.com/hakyimlab/MetaXcan for my UKB GWAS data and one tissue.

My question is how can I generate (and where do I download the data) to run:

./MetaXcan.py \
--model_db_path data/DGN-WB_0.5.db \
--covariance data/covariance.DGN-WB_0.5.txt.gz \
--gwas_folder data/GWAS \
--gwas_file_pattern ".*gz" \
--snp_column SNP \
--effect_allele_column A1 \
--non_effect_allele_column A2 \
--beta_column BETA \
--pvalue_column P \
--output_file results/test.csv

In particular how to create this file: covariance.DGN-WB_0.5.txt.gz

Cheers, Ana

ukb covariancematrix • 782 views
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