I am having a doubt with the function
FastaAlternateReferenceMarker from GATK. I already have a phased VCF file and when I want to obtain the fasta files for some specific genes (giving the target genes sequences and the VCF file to the function) I just obtain one of the sequences. This is okey for homozygous individuals, but I don't know how to obtain the two sequences for heterozygous individuals.
I've been checking the GATK website but I did not find anything, anybody else that had the same issue?
Thanks in advance!!