genome build for --extract bed1 file in PLINK
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4 months ago
eosimo • 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

build bed plink genome • 144 views
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Did you try bed0 instead of bed1?

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