How do I generate .bed file with PLINK from snps files and marker descriptions
Entering edit mode
7.9 years ago
haohanw ▴ 90

I have a task that is to generate .bed files from the files I have, but I am not sure how PLINK can do it.

What I have are two files, the SNP file is as following:

id: 1, 2, 3, 4, 5
1: A/A     G/G     A/A     A/A     A/A
2: G/G     A/A     A/A     NA      A/A
3: G/G     G/G     A/A     A/A     A/A
4: T/T     C/C     C/C     C/C     C/C

and I also have marker description file:

marker_rid      marker_name     marker_alleles  chrom   base_pair
1       MitoA10551G     A/G     M       10551
2       MitoA11252G     A/G     M       11252
3       MitoA11468G     A/G     M       11468
4       MitoA11813G     C/T     M       11813

Which means that I have 5 samples, each with a sequence length of 4.

Is there a command from PLINK that can allow me to do that?


bed plink SNP • 1.8k views

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