How to calculate expected Heterozygosity of Haploid organism?

Greetings!

I am dealing with NGS data. I have a vcf file of the called SNPs. I want to do population diversity and differentiation analysis with it but unfortunately, I unable to do so though I have tried using different software too. Can anyone help me in suggesting ways to do analysis using the vcf file?

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 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 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 ?

in the ARLEQUIN software the results of Population pairwise FSTs

were with negative value like -0.15254?

how the result was with negative value although fst should be between 0 and 1 ?

Hello,

I'm trying to create a genind object of an SNP dataset from Whelk to examine allelic richness between sites for some COI_16S sequences (combined sequences from the same individual).

My dataframe is in long format with individual SNPs coded as nucleotides(A, T, C, or G) and uninformative sites coded as "NA". There were two columns in the initial dataframe identifying specimens and populations that were selected out as a character vector "ind" and factor "popchar", respectively, and removed from the dataframe prior to converting. An additional character vector indicating loci names was also created, "locichar." The final dataframe contained the SNPs alone and was called "Whelk_SNP_file_dataonly".

Here is the code for the function df2genind():

df2genind(Whelk_SNP_file_dataonly, sep=" ", ploidy=1, ncode=1, ind.names=ind, loc.names=locichar, NA.char="NA", pop=popchar)

Each time I do this and look at the object using head(), I get this:

// 1 individual; 33 loci; 66 alleles; size: 15 Kb // Basic content @tab: 1 x 66 matrix of allele counts @loc.n.all: number of alleles per locus (range: 2-2) @loc.fac: locus factor for the 66 columns of @tab @all.names: list of allele names for each locus @ploidy: ploidy of each individual (range: 1-1) @type: codom @call: .local(x = x, i = i, j = j, drop = drop) // Optional content @pop: population of each individual (group size range: 1-1)

The file includes data from 242 individuals, not one. I cannot figure out why the function is reading my data as one individual. Does anyone have an idea of why adegenet is doing this and how I might fix it?

How to calculate heterozygosity ?

How to find suitable K value for determining genetic structure, I am using microsatellite markers.

I have used k from 1 to 10

Burnin Period 50000

MCMC rep 100000

How tocalculate delta K value using STRUCTURE

I have some genes with their FPKM values now i want to convert this value in to log2 fold change. 

Hello everyone,

I have a matrix of 170 genotypes and 3745 loci. I have added population origin to the matrix for further information when using adegenet package.

So, the first column is dedicated to genotypes (in rows), the second column is for "pop" and the third column is for locus1, fourth column is for locus2, etc. I have read adegenet tutorials.

I saved my file in a csv file. I loaded in R. All well.

The problem comes after I convert the data frame in a genind object. (I have 10 geographical origins on my data. The data frame is called adeg1):

h <- df2genind(adeg1, ploidy=2, pop=1:10, sep="/")

adegenet converts the data frame into a genind object called "h"

When I see my genind object:

h

/// GENIND OBJECT /////////

// 170 individuals; 3,747 loci; 7,670 alleles; size: 6.8 Mb

// Basic content

@tab: 170 x 7670 matrix of allele counts

@loc.n.all: number of alleles per locus (range: 2-170)

@loc.fac: locus factor for the 7670 columns of @tab

@all.names: list of allele names for each locus

@ploidy: ploidy of each individual (range: 2-2)

@type: codom

@call: df2genind(X = adeg1, sep = "/", pop = 1:10, ploidy = 2)

// Optional content

@pop: population of each individual (group size range: 1-1)

The loci number is not 3745 (seems that is counting the other two columns (genotype & pop)).

And, most important, when I try to use the function:

grp <- find.clusters(h, max.n.clust=40)

R retuns this:

pop is given but has invalid length

Error in validObject(x) : invalid class “genind” object: FALSE

I guess there is a problem with the "pop", because I set the original matrix without pop and grp function worked.

Can anyone help me?.

Thanks in advance,

Adelina.