UKB convert bgen to best guess plink format

bgen_to_plink.sh

#!/bin/bash

#!/bin/bash

for chr in {1..22}
do
  # Get the list of variants that pass the threshold
  bcftools filter -e 'INFO/R2<0.8' /mnt/project/Bulk/Imputation/Imputation\ from\ genotype\ \(TOPmed\)/helper_files/ukb21007_c${chr}_b0_v1.sites.vcf.gz | \
  bcftools filter -e 'INFO/AF<0.01' | \
  bcftools filter -e 'INFO/AF>0.99' | \
  bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%AF\t%R2\n' > variant_info_${chr}.txt

  cut -f 3 variant_info_${chr}.txt > variant_list_${chr}.txt
  awk '{print $1, $2, $2, $3}' variant_info_${chr}.txt | sort | uniq -u > variant_info_${chr}.range
  cut -f 3 variant_info_${chr}.txt > variant_list_${chr}.txt

  # Extract from plink
  plink2 \
      --bgen \"/mnt/project/Bulk/Imputation/Imputation from genotype (TOPmed)/ukb21007_c${chr}_b0_v1.bgen\" ref-first \
      --sample \"/mnt/project/Bulk/Imputation/Imputation from genotype (TOPmed)/ukb21007_c${chr}_b0_v1.sample\" \
      --extract range variant_info_${chr}.range \
      --maf 0.01 \
      --make-bed \
      --out ukb21007_b0_v1_c${chr}
done