Fst calculation with VCFtools

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6.4 years ago

Dracaena ▴ 50

Hi all!

I am working with 2 pools of full genome sequencing data. I currently have a VCF file for each pool and one VCF with the two combined (bcftools merge). Now I want to calculate the Fst for each SNP with vcftools, but I am a bit lost at this point. It says I have to provide one file for each population with a list of all individuals within one of those populations. I have used "bcftools query -l file.vcf" to see the samples in the merged files and it lists the correct two. When I use these two sample names in the .txt files for the Fst script it renders me an Fst saying "NA" at each locus... What am I doing wrong? Also, the "ID" column in my VCF is "."

Thanks!

vcftools fst pooled • 3.3k views

ADD COMMENT • link updated 2.1 years ago by Nasma • 0 • written 6.4 years ago by Dracaena ▴ 50

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Hi, Did you please find a solution to that problem ? I'm facing the same problem.

ADD REPLY • link 2.1 years ago by Nasma • 0

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