Question: Convert Plink files to UCSC BED files
gravatar for devenvyas
3.8 years ago by
Stony Brook
devenvyas630 wrote:

I have a Plink dataset, and I have been suggested to load it into UCSC Genome Browser (see for more details). To do so, I need to convert to BED/GFF/GTF files, and I have been told that BED files are the easiest.

I was wondering anyone here can show me how to do that? Thanks!

ucsc snp • 1.8k views
ADD COMMENTlink modified 3.8 years ago by Vincent Laufer1.1k • written 3.8 years ago by devenvyas630
gravatar for Vincent Laufer
3.8 years ago by
Vincent Laufer1.1k
United States
Vincent Laufer1.1k wrote:

I will answer this question with the hope of drawing out a bit more information - I think you will see why.

Assuming you have a .map file of the form:

 1  snp1   0  5000650

(that is chr SNP_ID GD Position)

and you want a .bed of the form specified in

you could write

awk '{print $1, $4-1, $4}' > my.bed

As this contains the 3 required fields to make a bed, it qualifies as a .bed file. However this exercise is nearly meaningless unless you then add annotations that you would like to view using UCSC.

Thus, if someone has suggested this to you, I am assuming that you have other files that give you some interesting values for each variant; ones that you might like to visualize. Is this the case?

ADD COMMENTlink written 3.8 years ago by Vincent Laufer1.1k
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