Question: Setting major allele in plink to plus strand of reference?
gravatar for curious
2 days ago by
curious310 wrote:

I have a plink file that someone gave me. I wan't to use it in an analysis where I know that the major allele needs to be set to the plus strand of the GRCh37 assembly.

I try:

plink2 --bfile {my_fav_file} --make-bed --ref-from-fa --fa {ref_fa} --out {my_fav_file_new}

I get:

Error: Unrecognized flag ('--ref-from-fa')

I did not copy paste any of the command and tried typing it out a few times. Am I misunderstanding what this command is supposed to do? Any help is greatly appreciated.

plink • 35 views
ADD COMMENTlink written 2 days ago by curious310

It looks like you need to update your plink2 build.

ADD REPLYlink modified 2 days ago • written 2 days ago by chrchang5237.0k

Ill give it a shot, thanks I was really scratching my head over this.

ADD REPLYlink written 1 day ago by curious310
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