Calculating allele frequency

[Dan Ravi]

Hi,

I ran my GWAS, but just noticed that allele frequency information was unfortunately missed, and I need it for a meta-analysis. I was curious if it is possible to estimate allele frequency information using the information that I have in my GWAS summary statistics file below, such as OBS_CT and OR? I know the number of cases and controls (binary phenotype) as well.

The columns of my GWAS summary statistics file are: CHROM, POS, ID, REF, ALT, A1, FIRTH, TEST, OBS_CT, OR, LOG(OR), SE, Z_STAT, and P.

If it is not possible to calculate using the above info, is it possible to use PLINK to generate only allele frequency data for each CHROM/POS? (I am running super low on my credits to run a new GWAS and would rather not re-run the entire GWAS to add FREQ...)

Thank you,

Dan

[Christopher Chang]

https://www.cog-genomics.org/plink/2.0/basic_stats#freq