VCF4.2 and/or Fst help

[Stephanie Schoeman]

Hi Chris,

I have a vcf file produced by Plink (v 4.3). I need to do Fst analysis so I tired using vcftools but it needs a vcf 4.2 or lower. 

That gave me 2 options:

1. convert to vcf v4.2 using pink (--export vcf-4.2) then use vcftools but then I get this error: Error: Require Genotypes in VCF file to output Fst statistics.

2. Use Plink to calculate fst to which I get the error: Note: No phenotype data present.

Error: --fst phenotype 'method=wc' not loaded.

If I include --within popfile .txt, what is the pop file format meat to be? 

I have attached both log files. I guess my question is, what would be the most efficient way to calculate the fst? 

If I include --within popfile .txt , what is the pop file format meat to be? 

Kind regards, 

Stephanie 

[Christopher Chang]

From https://www.cog-genomics.org/plink/2.0/input#within :

• The first two columns of this file must be FID/IID. By default, cluster names are loaded from column 3, but you can use --mwithin to change this to column (n+2).
• If no phenotype name is given, it defaults to 'CATPHENO'."