Question: How do I generate .bed file with PLINK from snps files and marker descriptions
0
gravatar for haohanw
3.0 years ago by
haohanw90
United States
haohanw90 wrote:

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?

Thanks.

snp plink .bed • 890 views
ADD COMMENTlink modified 3.0 years ago by geek_y9.8k • written 3.0 years ago by haohanw90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1615 users visited in the last hour