Question: Which tool to calculate nucleotide diversity stats?
2
gravatar for Ayité K
20 months 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 • 2.6k views
ADD COMMENTlink modified 20 months ago by lessismore600 • written 20 months ago by Ayité K30
1

See if this tutorial helps.

ADD REPLYlink written 20 months ago by h.mon24k
1
gravatar for lessismore
20 months ago by
lessismore600
Mexico
lessismore600 wrote:

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

ADD COMMENTlink written 20 months ago by lessismore600
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2412 users visited in the last hour