Prepare input data

Flink requires allele counts. We generally estimate those from genotype likelihoods using ATLAS (https://bitbucket.org/wegmannlab/atlas/wiki/alleleCounts). For that, you will need a VCF file that contains genotype likelihoods (e.g. the PL field).

If you do not have such a VCF file, you can also produce the required input file from the vcftools output below using awk: you just need to calculate the counts. You can do this with

vcftools -freq2 FILE | awk '{print $1, $2, $3*$4 "/" $3}'

However, this will only give you the frequencies for one population, so you will need to rerun it for each population (select samples with vcftools) and then join the files.