I am reading through the Eagle2 manual and came across this line in the description of phasing with a reference panel:
Eagle restricts analysis to sites that are contained in both the target and reference (with matching CHR, POS, and ALT fields) and are biallelic in the target VCF/BCF. Sites for which the REF and ALT alleles are swapped in the target VCF/BCF relative to the reference are dropped by default. This requirement can be relaxed via the --allowRefAltSwap flag, which causes REF/ALT swaps to be tolerated (and automatically flipped) for true SNPs
I'm a little confused about the second sentence. In what case would REF ALT swaps not want to be allowed? What do they mean by automatically flipped for true SNPs?
I tried googling but this flag does not have a lot of hits. I wish I could show progress towards understanding but I am kind of at a loss on this one and am seeking any kind of nudge in the right direction.