ukbb_gwas

#PLINK2 with dosages
for chr in 2 # {1..22}
do
 ./plink2 --bgen /mnt/ukbb/adam/bgen/ukb_imp_chr"$chr"_v3.bgen ref-first\
        --maf 0.01 \
        --geno 0.05 \
        --keep UKB_ptsd_eur_unrelated_m0_may13_2021.pheno \
        --sample /mnt/ukbb/adam/ptsd/preimputation_genotypes/ukb41209_imp_chr1_v3_s487320.sample \
        --pheno UKB_ptsd_eur_unrelated_m0_may13_2021.pheno --pheno-name PCL_sum_imp \
        --covar /mnt/ukbb/adam/ptsd/UKB_ptsd_eur_unrelated_m0_may13_2021_pcs.cov \
        --glm cols=chrom,pos,ref,alt,ax,a1freq,machr2,a1freqcc,firth,test,nobs,orbeta,se,ci,tz,p \
        --make-bed --out ukbb_gwas_name_here_"$chr"
done

Using best guess data
for chr in {1..22}
do
 ./plink2 --bfile /mnt/ukbb/adam/ptsd/bgeneur/ukbb_ptsd_bgen_eur_unrel_"$chr" \
         --maf 0.01 \
        --geno 0.05 \
        --pheno UKB_ptsd_eur_unrelated_m0_may13_2021.pheno --pheno-name PCL_sum_imp \
        --covar /mnt/ukbb/adam/ptsd/UKB_ptsd_eur_unrelated_m0_may13_2021_pcs.cov \
        --glm cols=chrom,pos,ref,alt,ax,a1freq,machr2,a1freqcc,firth,test,nobs,orbeta,se,ci,tz,p \
        --make-bed --out regular_ukbb_gwas_name_here_"$chr"
done



#BOLT LMM with dosages (outputs are different from PLINK)
  /mnt/ukbb/adam/ptsd/BOLT-LMM_v2.3.5/bolt \
    --bed=/mnt/ukbb/adam/ptsd/pca/UKB_ptsd_eur_related_{1..22}.bed \
    --bim=/mnt/ukbb/adam/ptsd/pca/UKB_ptsd_eur_related_{1..22}.bim \
    --fam=/mnt/ukbb/adam/ptsd/pca/UKB_ptsd_eur_related_1.fam \
    --LDscoresFile=/mnt/ukbb/adam/ptsd/BOLT-LMM_v2.3.5/tables/LDSCORE.1000G_EUR.tab.gz \
    --geneticMapFile=/mnt/ukbb/adam/ptsd/BOLT-LMM_v2.3.5/tables/genetic_map_hg19_withX.txt.gz \
    --numThreads=6 \
    --bgenFile=/mnt/ukbb/adam/bgen/ukb_imp_chr{1..22}_v3.bgen \
    --bgenMinMAF=1e-2 \
    --bgenMinINFO=0.8 \
    --sampleFile=/mnt/ukbb/adam/ptsd/preimputation_genotypes/ukb41209_imp_chr1_v3_s487320.sample \
    --verboseStats \
    --lmmForceNonInf \
    --statsFile=unimputed_output_filename_here.gz \
    --statsFileBgenSnps=imputed_output_filename_here.gz \
    --phenoFile=UKB_ptsd_eur_unrelated_m0_may13_2021.pheno \
    --phenoCol=PCL_sum_imp  \
    --covarFile=/mnt/ukbb/adam/ptsd/UKB_ptsd_eur_unrelated_m0_may13_2021_pcs.cov \
    --qCovarCol=PC{1:10}   \
    --remove /mnt/ukbb/adam/ptsd/bolt.in_plink_but_not_imputed.FID_IID.969.txt \
    --noBgenIDcheck