I have a VCF file, and I believe it is converted from PED file by PLINK, as illustrated in this blog:
There is one comment saying
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome">
in the VCF file.
For a some variant loci, the REF and ALT had been switched in the VCF file for unknown reason. For example, it should be G at locus 1234 in RefSeq, and the variant is T. But the VCF file records T(REF) and G(ALT).
I only have the VCF file, and do not have the original PED file. Is there any tool or method to check if the REF alleles are correct by RefSeq and switch REF and ALT columns (or just remove this loci) in the VCF if they're wrong?