Hello dears all, I am working on a whole genome data on a fish species. Now I want to calculate the allele frequency between pairs of populations and for this I tried to use the popoolation2. First the bam files were pooled using bamtools and then the protocol based on the website's guideline was proceed. But in the last step for the allele frequency calculation the command has been done incompletely. I thought it can be related to the RAM but it wasn't indeed. I also asked from the website but they did not answer. Now I am trying for an alternative way and I will be grateful if you can help me to make a go of this problem. Can vcftools do the allele frequency comparison between pairs of populations?
Any suggestion and command is appreciated already.