--- a
+++ b/gwas/plink_python_interface_gwas.sh
@@ -0,0 +1,16 @@
+bfile=/dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_all
+post_qc_snp=/dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_all_out-basic-qc.snplist
+post_qc_fam=/dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_all_out-basic-qc.fam
+result=/dfs/project/datasets/20220524-ukbiobank/data/result/
+covar=/dfs/project/datasets/20220524-ukbiobank/data/cohort/covar_pca15_all_real_value.txt
+pheno=$1
+
+./plink/plink2   --bfile ${bfile} \
+        --keep ${post_qc_fam} \
+        --extract ${post_qc_snp} \
+        --glm hide-covar \
+        --pheno ${pheno} \
+        --covar ${covar} \
+        --out "${result}$2" \
+        --memory 50000 \
+        --threads 20
\ No newline at end of file