Which tool to calculate nucleotide diversity stats?

Question

[Ayité K]

Hello,

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?.

[h.mon]

See if this tutorial helps.

Answer 1

[lessismore]

you can have a look at this: TASSEL http://www.maizegenetics.net/tassel you also have it command line.