A phylogenetic tree can be constructed directly from a VCF file. The simple software VCF2PopTree reads a VCF file and builds a tree in few minutes. It also produces pairwise distance matrix from a VCF file, which can then be used as an input file for the popular software such as MEGA.
Software: https://github.com/sansubs/vcf2pop
Paper: VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs. PeerJ, Vol.7, e8213; 2019
MEGA accepts fasta format files.
Check the following you may get useful information how to create fasta for VCF
Good Luck!!
VCF-kit Overview
(https://vcf-kit.readthedocs.io/en/latest/phylo/)
Generate fasta-alignment from variant calls
The phylo fasta command generates a fasta file by concatenating all single-nucleotide variants from a VCF for each sample. The first allele of each genotype is used (for example, for diploid organisms with an A/T genotype, A would always be used). Heterozygous calls should be avoided when using the phylo command. Missing values are replaced with a N. The fasta sequence is constructed in memory - so it can be somewhat resource intensive for larger files.
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