Plink recode option to get genomic position?

Question

[RNAseqer]

Is there a command to pull SNPs IDs and loci out of a bfile using plink? maybe something along the lines of the --recode option?

[Ram]

Is it not possible with plain awk? Is the bfile a binary file?

[RNAseqer]

It is a binary file yes.

Answer 1

[zx8754]

Plink binary format output has 3 files:

• bed - binary for genotypes
• bim - plain text map file for SNPs
• fam - plain text for samples.

2nd column of bim file is SNP id:

1. Chromosome code (either an integer, or 'X'/'Y'/'XY'/'MT'; '0' indicates unknown) or name
2. Variant identifier
3. Position in morgans or centimorgans (safe to use dummy value of '0')
4. Base-pair coordinate (1-based; limited to 231-2)
5. Allele 1 (corresponding to clear bits in .bed; usually minor)
6. Allele 2 (corresponding to set bits in .bed; usually major)

So we can get the second column, for example, using cut as:

cut -f2 myBim.bim > mySNPs.txt