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why do you think is deprecated? I see it on the manual
vcftoolsreceived its last update in 2018 where asbcftoolsis being actively developed.How to calculate Tajima's D using
bcftools: https://github.com/johnlees/tajima-DFair to mention that the windowed calculation is built-in in vcftools while you need to compile the app from github for use with bcftools.
You can use this tool called vcf2tajima https://github.com/xoaib4/vcf2tajima