Hello all, I'm a PLINK newbie. I am trying to extract a number of SNPs from a large imputation bgen file using the plink commands plink2 --bgen file.bge --sample sample.file --extract bed1 filewithcoordinatesofinterest.bed However it extracts the wrong coordinates, presumably as I have not had a chance to tell plink which reference genome the bed file is coded into? Can you specify the genome build? Is there any other tricks? Thanks for your help.