Cormac Kinsella comments

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                                            Cormac Kinsella

`vg call` strips path/contig info from vcf

I think this may be the same issue as #4442. I assumed I could run `vg call` without specifying a reference sample with `-S` (for a graph with only one...

`vg call` strips path/contig info from vcf

Thanks Glenn! That sounds like it would be pretty useful feature, as I'm not sure how to force sample ambiguity when there will only be one mapped sample handled per...

`vg call` strips path/contig info from vcf

P.S. I realise my suggestion wouldn't work as of course the PanSN notation is recreated in the pipeline - I'll do sed on the reference FASTA as you suggested