Question: Estimating population genetic parameters from SNP (genotype) data
2
gravatar for modi2020
4.5 years ago by
modi202040
United States
modi202040 wrote:

Dear Friends,

I am new to the plink SNPs data (genotypes) as I am used to work with markers.

I am wondering if there are any packages that can analyze basic pop gen parameters in SNP data such as DNASP and GenAlEx which are for microsatallite (sequences) data.

Specifically, I am interested in calculating Waterson's theta, FIS,FIT, FST, AMOVA, Tajima's D,and  the nucleotide diversity (pi). I know I can calculate these quantities in DNASP. Is there something corresponding to DNASP for SNP data.

I would really appreciate you guidance and suggestions with this.

 

Cheers

population genetics snp fst • 3.7k views
ADD COMMENTlink modified 4.5 years ago by Giovanni M Dall'Olio27k • written 4.5 years ago by modi202040

Thank you so much dschika.

I have plink genotypes on two horses populations.

I couldn't understand how to use genepop on them but I managed to use this tutorial which states that Hierarchical Fst tests is equal to AMOVA.

Do you know if Hierarchical Fst tests is equal to AMOVA?

Another question that bugs me is whether or not I can use all the genotypes at once. I have 30 thousand SNPs distributed on 31 chromosomes.

I really appreciate your help with this.

Thank you

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.5 years ago by modi202040

Sure, you can use all 30,000 SNPs at once. Most of the such R packages are designed to handle whole genome datasets.

ADD REPLYlink written 4.3 years ago by akang90
1
gravatar for dschika
4.5 years ago by
dschika300
European Union
dschika300 wrote:

Depending on the data format you have, e.g.:

vcftools

genepop

R-packages: adegenet, hierfstat

ADD COMMENTlink written 4.5 years ago by dschika300

Thank you so much dschika.

I have plink genotypes on two horse populations.

I couldn't understand how to use genepop on them but I managed to use the following tutorial (https://nescent.github.io/popgenInfo/DifferentiationSNP.html) which states that Hierarchical Fst tests is equal to AMOVA.

Do you know if Hierarchical Fst tests is equal to AMOVA?

Another question that bugs me is whether or not I can use all the genotypes at once. I have 30 thousand SNPs distributed on 31 chromosomes.

I really appreciate your help with this.

Thank you

ADD REPLYlink modified 9 months ago by RamRS27k • written 4.5 years ago by modi202040
1
gravatar for Giovanni M Dall'Olio
4.5 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

Since the data is in the plink format, have you tried plink? In alternative you can convert the data to vcf and use vcftools, for some of the stats you mentioned.

ADD COMMENTlink written 4.5 years ago by Giovanni M Dall'Olio27k

Thank you so much Giovanni. I will give that a shot as well.

ADD REPLYlink modified 9 months ago by RamRS27k • written 4.5 years ago by modi202040
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