cardio.txt

function CD6()
# SUMSTATS for depict
{
  gunzip -c $INTERVAL/INTERVAL_inf1_CD6___Q8WWJ7_chr_merged.gz | \
  awk -vOFS="\t" '(NR>1){
       SNP=$2;
       chr=$3; sub(/^0/,"",chr);
       pos=$4;
       a1=$5;
       a2=$6;
       N=$18;
       EAF=(0.5*$15+$16)/N;
       beta=$24;
       se=$25;
       p=$22;
       if(SNP!="." && p<=0.1) print SNP,a2,a1,EAF,beta,se,p,N,chr,pos;
  }' | \
  sort -k9,9n -k10,10n > CD6
}

export src=/scratch/bp406/data_sets/interval_subset_olink/genotype_files/unrelated_4994_pihat_0.1875_autosomal_imputed_info_0.4_phwe_1e-4_filtered/per_chr
export PERL5LIB=/scratch/jhz22/share/perl5

# INTERVAL data as LD reference
seq 22 | \
parallel --env src -j5 'plink --bfile $src/interval.imputed.olink.chr_{} --recode vcf bgz --out chr{}'
seq 22 | \
parallel -j5 'tabix -f -p vcf chr{}.vcf.gz'

## by chromosome worked through SLURM
sbatch --wait INTERVAL.sb
plink --bfile UK10K1KG-6 --chr 6 --from-mb 25 --to-mb 35 --make-bed --out MHC
cut -f2 MHC.bim > MHC.snpid
seq 22 | \
awk -vp=$PWD '{print p "/UK10K1KG-" $1}' > INTERVAL.list
plink --merge-list INTERVAL.list --make-bed --out INTERVAL

## whole-genome version, too slow to run
# seq 22 | \
# awk -vp=$PWD '{print p "/chr" $1 ".vcf.gz"}' > INTERVAL.list
# bcftools concat --file-list INTERVAL.list --threads 6 | \
# bcftools annotate --set-id 'chr%CHROM\:%POS\_%REF\_%ALT' --threads 6 - -O z -o INTERVAL.vcf.gz
# plink --vcf INTERVAL.vcf.gz --make-bed --out INTERVAL

## side information
export PHEN=/scratch/curated_genetic_data/phenotypes/interval/high_dimensional_data/Olink_proteomics_inf/gwasqc/olink_qcgwas_inf.csv
export IMPUTED=/scratch/curated_genetic_data/interval/imputed
function reference()
{
  cut -d"," -f1 $PHEN | \
  awk 'NR>1 {OFS="\t";print $1,$1}' > INTERVAL.id
  seq 22 | \
  parallel -j3 --env IMPUTED -C' ' '
    plink --bgen $IMPUTED/impute_{}_interval.bgen \
          --sample $IMPUTED/interval.samples \
          --keep INTERVAL.id \
          --make-bed \
          --out INTERVAL-{} \
          --threads 2
  '
}

export SCRIPT=/scratch/jp549/analyses/interval_subset_olink/inf1/r2/outlier_in/pcs1_3
export BS=/scratch/jp549/apps/bram-scripts

# \\me-filer1\groups$\MGEU\Factors\High_dimensional_genetics\Olink\INF1
# /scratch/bp406/data_sets/interval_subset_olink/genotype_files/unrelated_4994_pihat_0.1875_autosomal_imputed_info_0.4_phwe_1e-4_filtered/per_chr