I know there are already quite a lot of posts explaining how to convert a VCF file to Fasta (In fact, I was using FastaAlternateReferenceMarker) but I did not find any solution for what I want to do. I have a multisampled and phased VCF file and I want to convert each one of the samples that are combined in my VCF to Fasta files. When I do the GATK command, I just obtain one fasta file. I would really appreacite your help!!