Question: How to get independent loci from gwas variants
0
gravatar for morse.endeavour86
12 days ago by
morse.endeavour860 wrote:

Hi all,

I am new to bioinformatic analysis and need to get independent loci from gwas variants.

Is there any script/tool which allows me to take those variants say in 2 or 3 Mb windows and then find independent loci/regions from them using correlation values etc? Or is there any method for doing this?

Thanks, Chithra

sequencing snp R python gwas • 88 views
ADD COMMENTlink modified 12 days ago • written 12 days ago by morse.endeavour860

find independent loci/regions

What does that mean?

ADD REPLYlink written 12 days ago by WouterDeCoster45k

Ahh by independent loci I just mean that as I have thousands of variants I from gwas, I would now like to aggregate them into distinct regions aka genomic loci. And I was wondering whether there is any tool/script etc, which allows one to get loci from variants.

ADD REPLYlink written 12 days ago by morse.endeavour860

Then you probably want to combine variants which are close to each other?
Have a look at bedtools merge with -d for a certain distance which you consider 'sufficiently close'.

ADD REPLYlink written 12 days ago by WouterDeCoster45k

Thanks for yoru reply. But this method needs a bed file which I don't have. The only thing I have is the GWAS summary stats.

ADD REPLYlink written 12 days ago by morse.endeavour860

It should not be hard to convert that to a valid bed format. It is also always helpful to show an example of the data you have.

ADD REPLYlink written 12 days ago by WouterDeCoster45k
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