BWAS analyses - real UKB phenotypes
by [Baptiste Couvy-Duchesne] - 13 June 2022 -
1 Create environment
wd="/path/to/working/directory"
cd $wd
mkdir -p ${wd}/03_BWAS_uncorrected_realPheno
mkdir -p ${wd}/09_BWAS_ICVagesex_realPheno
mkdir -p ${wd}/04_BWAS_5globalPCs_realPheno
mkdir -p ${wd}/05_BWAS_10globalPCs_realPheno
mkdir -p ${wd}/06_BWAS_10specificPCs_realPheno
mkdir -p ${wd}/07_BWAS_MOA_realPheno
mkdir -p ${wd}/15_BWAS_MOA_allModa_FE_realPheno2 GLM no covariates
We have created a text file UKB_BWASvars.txt, which contains the list of variables we want to study. This file is used to loop on the phenotypes of interest.
wd="path/to/working/directory"
cd $wd/03_BWAS_uncorrected_realPheno
${wd}/qsubshcom "
phenotype=\$(sed -n \"\${TASK_ID}{p;q}\" "${wd}"/UKB_BWASvars.txt) |;
echo \${TASK_ID} |;
echo \${phenotype} |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/UKB_phenotypes15K/\${phenotype}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --linear --out "${wd}"/03_BWAS_uncorrected_realPheno/BWAS_\${phenotype} |;
" 1 50G BWAS03_realPheno 24:00:00 "-array=6-96 " 3 GLM with 5 global PCs
wd="path/to/working/directory"
cd $wd/04_BWAS_5globalPCs_realPheno
${wd}/qsubshcom "
phenotype=\$(sed -n \"\${TASK_ID}{p;q}\" "${wd}"/UKB_BWASvars_5pheno.txt) |;
echo \${TASK_ID} |;
echo \${phenotype} |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/UKB_phenotypes15K/\${phenotype}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --linear --qcovar "${wd}"/PC.5global.eigenvec --out "${wd}"/04_BWAS_5globalPCs_realPheno/BWAS_\${phenotype} |;
" 1 50G BWAS04_realPheno 24:00:00 "-array=1-5 " 4 GLM with 10 global PCs
wd="path/to/working/directory"
cd $wd/05_BWAS_10globalPCs_realPheno
${wd}/qsubshcom "
phenotype=\$(sed -n \"\${TASK_ID}{p;q}\" "${wd}"/UKB_BWASvars.txt) |;
echo \${TASK_ID} |;
echo \${phenotype} |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/UKB_phenotypes15K/\${phenotype}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --linear --qcovar "${wd}"/PC.10global.eigenvec --out "${wd}"/05_BWAS_10globalPCs_realPheno/BWAS_\${phenotype} |;
" 1 50G BWAS05_realPheno 24:00:00 "-array=1-96 " 4.1 Combine the summary statistics so they have the same format as others
wd="path/to/working/directory"
cd $wd/06_BWAS_10specificPCs_realPheno
${wd}/qsubshcom "
phenotype=\$(sed -n \"\${TASK_ID}{p;q}\" "${wd}"/UKB_BWASvars_5pheno.txt) |;
echo \${TASK_ID} |;
echo \${phenotype} |;
tail -n +1 "${wd}"/06_BWAS_10specificPCs_realPheno/BWAS_\${phenotype}_thickness.linear > "${wd}"/06_BWAS_10specificPCs_realPheno/BWAS_\${phenotype}.linear |;
for moda in area thick LogJacs |;
do |;
tail -n +2 "${wd}"/06_BWAS_10specificPCs_realPheno/BWAS_\${phenotype}_\${moda}.linear >> "${wd}"/06_BWAS_10specificPCs_realPheno/BWAS_\${phenotype}.linear |;
done |;
" 1 4G BWAS_realPheno_putTogether 01:00:00 "-array=1-5 " 5 GLM with 10 specific PCs
wd="path/to/working/directory"
cd $wd/06_BWAS_10specificPCs_realPheno
${wd}/qsubshcom "
phenotype=\$(sed -n \"\${TASK_ID}{p;q}\" "${wd}"/UKB_BWASvars.txt) |;
echo \${TASK_ID} |;
echo \${phenotype} |;
for moda in area thickness thick LogJacs |;
do |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.\${moda}.fwhm0.fsaverage.UKB15K --pheno "${wd}"/UKB_phenotypes15K/\${phenotype}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --linear --qcovar "${wd}"/PC.10specific.\${moda}.eigenvec --out "${wd}"/06_BWAS_10specificPCs_realPheno/BWAS_\${phenotype}_\${moda} |;
done |; " 1 40G BWAS06_realPheno 24:00:00 "-array=1-96 " 6 LMM single random effect
wd="path/to/working/directory"
cd $wd/07_BWAS_MOA_realPheno
${wd}/qsubshcom " if [ ! -f "${wd}"/07_BWAS_MOA_realPheno/BWAS_\${phenotype}.moa ] |;
then |;
phenotype=\$(sed -n \"\${TASK_ID}{p;q}\" "${wd}"/UKB_BWASvars.txt) |;
echo \${TASK_ID} |;
echo \${phenotype} |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/UKB_phenotypes15K/\${phenotype}.phen --orm "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC --remove "${wd}"/ID_UKB_replication.txt --moa --out "${wd}"/07_BWAS_MOA_realPheno/BWAS_\${phenotype} |;
fi " 1 60G BWAS07_realPheno 24:00:00 "-array=1-5 " 7 GLM with ICV, age and sex as covariates
wd="path/to/working/directory"
cd $wd/09_BWAS_ICVagesex_realPheno
${wd}/qsubshcom "
phenotype=\$(sed -n \"\${TASK_ID}{p;q}\" "${wd}"/UKB_BWASvars.txt) |;
echo \${TASK_ID} |;
echo \${phenotype} |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/UKB_phenotypes15K/\${phenotype}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --linear --qcovar "${wd}"/ageSexIcv.txt --out "${wd}"/09_BWAS_ICVagesex_realPheno/BWAS_\${phenotype} |;
done |; " 1 50G BWAS09_realPheno 24:00:00 "-array=1-5 "
# Sex, age and ICV BWAS
wd="path/to/working/directory"
cd $wd/09_BWAS_ICVagesex_realPheno
${wd}/qsubshcom "
for phenotype in Age_MRI sexuses_datacoding_9_f31_0_0 ICV |;
do |;
echo \${phenotype} |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/UKB_phenotypes15K/\${phenotype}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --linear --qcovar "${wd}"/UKB_phenotypes15K/Covariates_no_\${phenotype}.phen --out "${wd}"/09_BWAS_ICVagesex_realPheno/BWAS_\${phenotype} |;
done |; " 1 50G BWAS09_realPheno_ageSexICV 24:00:00 "" 8 LMM with covariates
wd="path/to/working/directory"
cd $wd/15_BWAS_MOA_allModa_FE_realPheno
${wd}/qsubshcom "
phenotype=\$(sed -n \"\${TASK_ID}{p;q}\" "${wd}"/UKB_BWASvars_5pheno.txt) |;
echo \${TASK_ID} |;
echo \${phenotype} |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/UKB_phenotypes15K/\${phenotype}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --moa --qcovar "${wd}"/ageSexIcv.txt --out "${wd}"/15_BWAS_MOA_allModa_FE_realPheno/BWAS_\${phenotype} |;
done |; " 1 100G BWAS09_realPheno 24:00:00 "-array=1-5 "
# Sex, age and ICV BWAS
wd="path/to/working/directory"
cd $wd/15_BWAS_MOA_allModa_FE_realPheno
for phenotype in sexuses_datacoding_9_f31_0_0
do
${wd}/qsubshcom "
echo ${phenotype} |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/UKB_phenotypes15K/${phenotype}.phen --orm "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC --remove "${wd}"/ID_UKB_replication.txt --moa --qcovar "${wd}"/UKB_phenotypes15K/Covariates_no_${phenotype}.phen --out "${wd}"/15_BWAS_MOA_allModa_FE_realPheno/BWAS_${phenotype} |; " 1 100G BWAS15_${phenotype}_ageSexICV 24:00:00 ""
done9 LMM several random effects
wd="path/to/working/directory"
cd $wd/10_BWAS_MOA_multiORM_QC_realPheno
${wd}/qsubshcom "
phenotype=\$(sed -n \"\${TASK_ID}{p;q}\" "${wd}"/UKB_BWASvars.txt) |;
echo \${TASK_ID} |;
echo \${phenotype} |;
if [ ! -f "${wd}"/10_BWAS_MOA_multiORM_QC_realPheno/BWAS_\${phenotype}.moa ] |;
then |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/UKB_phenotypes15K/\${phenotype}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --moa --multi-orm "${wd}"/fwhm0.fsaverage.QC.ormlist --out "${wd}"/10_BWAS_MOA_multiORM_QC_realPheno/BWAS_\${phenotype} --reml-no-constrain |;
fi |;
" 1 60G BWAS10_allPheno 48:00:00 "-array=1-5 " A work by by [Baptiste Couvy-Duchesne] - 13 June 2022