Hi guys
I recently received a VCF file containing SNP information but it seems to have the allele information solely depending on population. (They basically placed more observed allele in my sample as REF) Therefore, the file has 'Major Allele' on REF and 'Minor Alleles' on ALT. Is there any shared script that can convert this file into correct REF/ALT format using reference genome?
+1 "REF part is chosen based on the reference sequence"
My brain kinda goes bonkers after midnight, I guess. Did I phrase it weird? I do hope the phrasing did not introduce ambiguity to the fact underneath.