Question: Reverse allele frequency
0
gravatar for panacotaforcota
7 months ago by
Russia
panacotaforcota0 wrote:

Hello!

I have a problem with reverse allele frequency in my GWAS. I compare the allele frequency of SNP from GWAS with reference allele frequency. My results after synchronization allele:

X - reference frequency; Y - GWAS frequency

So, I want to understand how I can detect such SNPs to remove them from the analysis. Maybe there are common approaches.

allele frequency gwas • 245 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by panacotaforcota0

how did you synchronize ?

ADD REPLYlink written 7 months ago by Nicolas Rosewick9.3k

By my own script. Briefly, I change allele frequency as (1-freq) in the reference data if alleles were reverse, for example, in GWAS - A:T, in reference - T:A. There is no mistake.

ADD REPLYlink written 7 months ago by panacotaforcota0

could you post your code ? Are you comparing the allele freq to gnomAD ?

ADD REPLYlink written 7 months ago by Nicolas Rosewick9.3k

it could be that the reference is given as "mAF", minor allele frequency. Trying to "reverse" in this case will lead to such picture.

ADD REPLYlink written 7 months ago by German.M.Demidov1.9k

But X and Y axis from 0 to 1. In MAF case 0.5 is upper limit.

ADD REPLYlink written 7 months ago by panacotaforcota0

Unless one tries to "revert" something...

Not sure if it is the cause, but worth to be checked.

the reference data if alleles were reverse, for example, in GWAS - A:T, in reference - T:A

ADD REPLYlink written 7 months ago by German.M.Demidov1.9k
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