I have made a vcf file with GATK that include SNPs from 10 samples.
My goal is to make a phylogenetic tree of SNPs,
Can you redirect me toward a ressource than explain what is the possibilities from a VCF file ?.
I have imagined making a fasta file and feed it to phylogenetic inference tool such as RAxML.
Did you guys have experienced with this kind of work ?
Thanks a lot.