sample code for running BOLTLmm

tin_gwas1

  BOLT-LMM_v2.3.2/bolt \
    --bed=pca/UKB_tinnitus_eur_unrelated_{1..22}.bed \
    --bim=pca/UKB_tinnitus_eur_unrelated_{1..22}.bim \
    --fam=pca/UKB_tinnitus_eur_unrelated_1.fam  \
    --LDscoresFile=BOLT-LMM_v2.3.2/tables/LDSCORE.1000G_EUR.tab.gz \
    --geneticMapFile=BOLT-LMM_v2.3.2/tables/genetic_map_hg19_withX.txt.gz \
    --lmmForceNonInf \
    --numThreads=6 \
    --bgenFile=/mnt/ukbb/adam/bgen/ukb_imp_chr{1..22}_v3.bgen \
    --bgenMinMAF=1e-3 \
    --bgenMinINFO=0.3 \
    --sampleFile=ukb40951_imp_chr1_v3_s487324.sample \
    --verboseStats \
    --modelSnps all.pruned \
    --remove bolt.in_plink_but_not_imputed.FID_IID.968.txt \
    --noBgenIDcheck \
    --statsFile=f.4803.max_coding1_allcov_unrelated.bed.stats.gz \
    --statsFileBgenSnps=zf.4803.max_coding1_allcov_unrelated.bgen.stats.gz \
    --phenoFile=UKB_tinnitus_eur_unrelated_april2_2019.pheno \
    --phenoCol=f.4803.max_coding1 \
    --covarFile=UKB_tinnitus_eur_unrelated_april2_2019.pheno \
    --qCovarCol=f.2247.max_coding1 --qCovarCol=f.21003.max --qCovarCol=f.31.0.0 --qCovarCol=f.22009.0.{1:6} --covarCol=f.54.0.0 --covarCol=f.22000.0.0 \
    --covarMaxLevels=107