Question: Which tool to calculate nucleotide diversity stats?
2
gravatar for Ayité K
2.1 years ago by
Ayité K30
France
Ayité K30 wrote:

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?.

snp stats diversity • 3.2k views
ADD COMMENTlink modified 2.1 years ago by lessismore670 • written 2.1 years ago by Ayité K30
1

See if this tutorial helps.

ADD REPLYlink written 2.1 years ago by h.mon27k
1
gravatar for lessismore
2.1 years ago by
lessismore670
Mexico
lessismore670 wrote:

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

ADD COMMENTlink written 2.1 years ago by lessismore670
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