No reference strain in output alignment file?

[nghait]

The tool is very convenient and memory efficient. I'm new to the coding, but is there any way to also output the reference into alignment fasta file. With the following command, I get only the strains but not the reference strain in the concatenated variants in alignment fasta format. $ vk phylo fasta my_multiple_strains.vcf > my_alignment.fasta

Thank you for your contribution.

[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