Hi, I have 22 chromosome .bgen files separately. For PRS, i want to merge them using -pmerge. For that I need bcf formats. So basically I'm at 1st stage, converting .bgen to bcf and quality control. But after giving command, I'm getting error message - ' Error: Only VCF, oxford, bgen-1.x, haps, hapslegend, A, AD, A-transpose, and ind-major-bed output have been implemented so far.' My command -
plink2 \ --bgen /mnt/d/ukb_genetic_data/ukb_imp_chr1_v3.bgen ref-first \ --sample /mnt/d/ukb_genetic_data/ukb30172_imp_chr22_v3_s487324.sample \ --maf 0.01 \ --hwe 1e-6 \ --geno 0.01 \ --mind 0.01 \ --export bcf \ --out chr101
Thanks for your help.