Entering edit mode
3.9 years ago
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
What does that mean?
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.
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'.
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.
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.