Entering edit mode
2.9 years ago
eosimo
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0
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.
Emanuele
Did you try bed0 instead of bed1?