Change ALT/REF allele in plink

Question

[alessandro]

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?

Answer 1

[chrchang523]

Please read the --ref-allele documentation (plink2 treats --a2-allele and --ref-allele the same way). If that's hard to interpret, read https://www.cog-genomics.org/plink/2.0/general_usage first.