No reference strain in output alignment file? about vcf-kit

[danielecook]

Hey nghait - I believe I followed up via email. My recommendation would be to add the reference to the VCF file. If you are having trouble please let me know.

[nghait]

Great Daniel,
My acknowledgement.

[vappiah]

@danielecook I would be grateful if you can show how to add the reference sequence to the vcf file.
Is it also possible to add the reference sequence to the newly generated fasta file and pass it to vk for the phylogenetic tree to be drawn? If not, can you add a feature that can do that? Thanks