extract list of SNPs from multiple chr{1:22}.bgen files using plink2

Question

[Sharad]

hello, I have extracted out list of snps based on the maf cutoff 0,,0.0001, 0.001,0.01,0.1,.55,1.0. I am running plink2 to extract this list from .bgen files for individual chromosomes using the following code

plink2 \
 --chr{1:22}.bgen \
 --extract maf1_snps for imputed data.txt \
 --export bgen-1.2 \
 --out maf1_snps

i get error Error: Unrecognized flag ('--chr{1:22}.bgen'). For more info, try "plink2 --help <flag name>" or "plink2 --help | more".

I would appreciate any help to resolve. Thx

Answer 1

[chrchang523]

You need to slow down and spend some time working through a tutorial or reading documentation before proceeding. There are multiple problems with your command line which indicate that you haven't learned the basics yet.