VCF tags for reference and contigs
The VCF header does not properly set the chromosome name. It currently uses the fasta header as such (rather than assigning it the proper number and adding that annotation to the VCF header). While this doesn't create any issues for using the output with bcftool or vcftools, vcf-validator complains:
The header tag 'reference' not present. (Not required but highly recommended.)
The header tag 'contig' not present for CHROM=gi|448814763|ref|NC_000962.3|. (Not required but highly recommended.)