extract based on position

[Robert Corty]

Hi all,

I would like to extract some SNPs from my psam,pvar,pgen files. I have the chromosome and position of all the SNPs, but not the rsID.

I have tried using this approach:

Options in effect:
  --extract range MYSNPFILE
  --make-bed
  --out MYOUTFILE
  --pfile MYPSAM,PVAR,PGENFILES

and was met with this error:

Error: Invalid chromosome code on line 1 of --extract bed1 file.

Here's the entirety of my snp file that I am currently using... (I have other files with more rows)

CHR     BP1     BP2
12      112090022       112090022

Another approach I tried was using  "12:112090022" as the ID, but that left me with no matching SNPs. (I have verified manually that this SNP is in the pvar file).

Any help would be much appreciated!

Robert

[Christopher Chang]

plink does not currently expect a header line in this file.  I'll probably modify plink2 soon to tolerate one header line starting with "chrom", any capitalization.

[Christopher Chang]

Actually, it looks like I made this modification two years ago; if you are using a build from January 2020 or earlier, can you update and retry?