I have SNPs data in several vcf files and I would like to compute diversity stats like Pi, Tajima'D, Theta, ... .
I have tryed vcftools which actually worked but all stats are not available. I am trying dnaSP with my data formated to fasta format. DnaSP is not a command line tool and it can't handle directly fasta format with IUPAC code representing Hz data. It has a sequence reconstruction step before one can compute the stats.
So does anyone know a tool (preferably a command line tool) or a R package using vcf file (or formated to any other format) to calculate diversity stats like Pi, theta, Tajima'D ?
Which tool to calculate nucleotide diversity stats?.