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@ -11,12 +11,12 @@ Version of PLINK: PLINK v1.90b3.32 64-bit (24 Feb 2016)
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#Step 1: load PLINK module:
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#Step 1: load PLINK module:
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--module load plink/v1.90b3.32
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--module load plink/v1.90b3.32
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# Step 2: Perform association analyses between IL33 (imputed) genotype (400kb region, defined by start/stop SNP) and phenotype:
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# Step 2: Perform association analyses between IL33 (imputed) genotype (400kb region, defined by start/stop SNP) and phenotype:
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## 2a LIFELINES/DAG?GASP individual cohorts: Binary or continous phenotype:
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## 2a LIFELINES/DAG?GASP individual cohorts: Binary or continous phenotype:
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--plink --noweb --fam "file.fam" --allow-no-sex --dosage "imputedgenofile.dose" noheader format=2 Zin --map "file.bim" --from rs61134586 --to rs73639329 --pheno "phenofile.dat" --missing-phenotype -9 --covar "covarfile.dat" --out "outfile.txt" --ci 0.95
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--plink --noweb --fam "file.fam" --allow-no-sex --dosage "imputedgenofile.dose" noheader format=2 Zin --map "file.bim" --from rs61134586 --to rs73639329 --pheno "phenofile.dat" --missing-phenotype -9 --covar "covarfile.dat" --out "outfile.txt" --ci 0.95
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###The phenotype is in the *.fam files. In the cov_XXX.txt files the covariates gender and age are included
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###The phenotype is in the *.fam files. In the cov_XXX.txt files the covariates gender and age are included
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