How to get independent loci from gwas variants

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3.3 years ago

morse.endeavour86 • 0

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

gwas R snp sequencing python • 747 views

ADD COMMENT • link 3.3 years ago by morse.endeavour86 • 0

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find independent loci/regions

What does that mean?

ADD REPLY • link 3.3 years ago by WouterDeCoster 47k

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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 REPLY • link 3.3 years ago by morse.endeavour86 • 0

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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 REPLY • link 3.3 years ago by WouterDeCoster 47k

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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 REPLY • link 3.3 years ago by morse.endeavour86 • 0

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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 REPLY • link 3.3 years ago by WouterDeCoster 47k

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