Estimating population genetic parameters from SNP (genotype) data

Question

[modi2020]

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

[modi2020]

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

[akang]

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

Answer 1

[dschika]

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

vcftools

genepop

R-packages: adegenet, hierfstat

[modi2020]

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

Answer 2

[Giovanni M Dall'Olio]

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.

[modi2020]

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