Reorienting 1000 Genome VCF files, so that derived alleles are always ALT

Question

[devenvyas]

Hello,

I am working with the 1000 Genomes Project phase 3 VCF files. I am trying to figure out how to reorient the REF and ALT alleles so that the derived allele is always the ALT.

I tried the --derived option in vcftools, but that apparently does nothing for the VCF output files.