I am working with allele frecuencies and his changes over the time. I noted that the allele of interest sometimes is in ALT column and sometimes in REF column.
I tried using
plink2 --file data --a2-allele rs3094315 --freq --out test1
to test if this command can change the frecuence of my allele (REF: G/ ALT: A to REF:A / ALT:G) to give me te frecuence of the ALT allele but it does'nt work. How can i get the frecuence of this alleles of my interest changing the REF/ALT allele in plink?