FASTA file

plotVCF was developed based on Human genome. Thus, in case you are analyzing Human data in hg19 or hg38 assembly, you do not need to pass any FASTA file, as plotVCF already known genome coordinates. Default plotVCF assembly is Human hg38

On the other side, if you wish to use plotVCF with a different species or assembly, you need a FASTA file to let the software know chromosome boundaries etc.

You need to use the same FASTA format on which your VCF was aligned to. If you are not sure, you should find this information in your VCF header

Important: make sure the chromosome names in your FASTA file exactly match chromosome names in your VCF file! (e.g. you can find VCF with chr1 name format while FASTA may have 1 name format, or reversal. Those VCF and FASTA chromosome names must exactly match!)