Create consensus sequence by applying VCF variants to a reference fasta file.
http://samtools.github.io/bcftools/bcftools.html#consensus
https://github.com/samtools/bcftools/wiki
The option to set the new consensus' FASTA ID from the name of the VCF is provided by post-processing the bcftools consensus output. It is primarily intended for use when the VCF is coming from a list collection where the elements of the list are named meaningfully (e.g. named after sample names). This is useful when consensus sequences are being prepared for, for example, feeding a multiple sequence alignment to a phylogeny program.