In VCF, the ALT column is supposed be where you show what variants you found. Or, as implied in the spec and all the example files I've seen, the ALT column shows all the non-reference variants you found.
But if I'm sequencing a sample and want to use VCF to store its variant calls, I'd like to be able to explicitly say "I did find the REF allele here" and "I did not find the REF allele there."
1) Is it valid to put the REF allele in the ALT column, and
2) regardless of validity, do common tools explode if they encounter this situation?