Entering edit mode
3.4 years ago
Sharad
▴
10
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