How to Generate VCF from two FASTA genomes?
I am wondering if there is a way/tool to align two multi-chromosome genomes in FASTA format and call variants into a VCF. I am trying to determine variants between two strains of Plasmodium falciparum (malaria parasite), which should be vastly identical with relatively few variants, and we have assembled genomes for both stains.
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You could use
minimap2to align the data and then call variants. If chromosomes are well defined in each genome then you could do one to one alignments in order to prevent all sorts of secondary alignments elsewhere,