Heterozygous individuals and FastaAlternateReferenceMarker

Question

[gubrins]

Good afternoon,

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!!