Reverse allele frequency
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:
So, I want to understand how I can detect such SNPs to remove them from the analysis. Maybe there are common approaches.
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panacotaforcota •
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how did you synchronize ?
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.
could you post your code ? Are you comparing the allele freq to gnomAD ?
it could be that the reference is given as "mAF", minor allele frequency. Trying to "reverse" in this case will lead to such picture.
But X and Y axis from 0 to 1. In MAF case 0.5 is upper limit.
Unless one tries to "revert" something...
Not sure if it is the cause, but worth to be checked.