Good afternoon, I'm working with a lizard species and we did a target capture sequencing for the nuclear genes related in the OXPHOS process and the mitochondrial genome. What I want to have are the haplotypes for each of my samples, so I can do phylogenetic and other type of analyses, but I'm struggling with Beagle to obtain them.
I already have the VCF file for each of my samples (which is required by Beagle) and I have my target genes in fasta format. I was reading that I have to phase them and convert them to bref3, is that right? After I run them, what do I obtain? I'm also not understanding properly the output of beagle, as I'm running the example dataset and I don't see the haplotypes in the output. I was checking for tutorials but seems that people is okey just with the manual, I suppose that I'm not used to these programs yet, sorry for that.