Multisample VCF to FASTA · Biostar

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Multisample VCF to FASTA

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!!

vcf fasta gatk

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updated 6.2 years ago by Kevin Blighe

• written 6.2 years ago by gubrins

1 answer

Hi,

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

Kevin

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written 6.2 years ago by Kevin Blighe

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