You need an additional Map file. With that, plink should be able to convert your files automatically.
Example from Plink's own "toy" data:
(without header) CHR SNP-ID cM_Position(set to 0) BP_position
1 rs0 0 1000
1 rs10 0 1001
just create this file with a line for each of your markers and without the header, and it should work.
plink command example:
"plink --file INPUT --make-bed --out OUTFILE"
Plink will create a "binary" set of three files:
- .fam - phenotype information for each sample
- .bed - binary genotype file
- .bim - map file
The map file will contain additional columns for your genotype alleles, coded with 0/1/2. You may later change that if you like, see "https://www.cog-genomics.org/plink/1.9/data#update_map"
Some additional tips:
- If you don't have a family ID, use the sample ID for the family ID as well. For now, al your samples belong to family "0"
- Use Plink 2.0, it is much faster. Keep Plink 1.07 as a backup copy somewhere, some features of Plink 1.07 are not implemented in Plink 2 yet
modified 2.8 years ago
2.8 years ago by
MoppelKopp • 0