I have a plink 2.0 file ("Ref" is always the major allele) and want to reorder its ref and alt alleles by a fasta reference. For this I use the --ref-from-fa command. However, the following error occurs:
Error: --ref-from-fa wants to change reference allele assignment at X:2700157,but it's marked `as 'known'. Add the 'force' modifier to force this change`
What does marked as "known" mean? How should I go on?