If you don't need the read depth information then it might be easier to parse the .loci file, which has the length and highlights variable site columns. The full VCF is usually really really huge, since it stores so much extra information, so unless you're interested in that info it's not ideal. And most (all?) other programs seem to only output VCF for variable sites. But, since we do currently support it I think we should be able to fix it and make it work again for now if you want it.