genome build for --extract bed1 file in PLINK
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
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chrchang523
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eosimo •
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eosimo •
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Did you try bed0 instead of bed1?