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I'm not sure how well this is supported in the VCF spec or parsers, but it would be very helpful to present information about the genome assembly.
In practise the useful information will probably be in the contig header, and the actual assembly
header won't be much use if it's just referring to a fasta file. The VCF spec gives these examples:
##assembly=url
##contig=<ID=ctg1,length=81195210,URL=ftp://example.com/assembly.fa,md5=f126cdf8a6e0c7f379d618ff66beb2da,...>
I guess all we can do is keep the information about the assembly and contig around as attributes so that they can be easily inspected?
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