Heterozygosity levels small sample size

Question

[pkotsakiozi]

Hello all,

I was wondering what is the best way to compare the heterozygosity levels in my data set for which I have ~70,000snps but 4 individuals per population. I am actually interested in comparing the heterozygosity levels between the main broad groups of populations (for each group I have 5-10 populations) and not between the actual populations.

Thank you very much for your help in advance.

Answer 1

[Patrick Brennan]

Is this data in VCF file format? It seems like the best way to achieve your goal is to write a Perl or Python script.