I have a multi-sample vcf file with ~7 millions SNPs. Now I want to convert it into required format of the Treemix. I run it using
vcf2treemix.sh along with
plink2treemix.py, but plink2treemix.py works very very slow. So that if I use it, the analysis in question may take more than a month or even longer.
Does anyone of you have a solution to increase the speed of this program or a better suggestion to do this analysis