Multisample VCF to FASTA

Question

[gubrins]

Good afternoon,

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!!

Answer 1

[Kevin Blighe]

Hi,

You could consider splitting your VCF into multiple samples and then running the command multiple times for each VCF.

Kevin