Hi,
I am using PopGenome to compare statistics such as Fst, nucleotide diversity, and Tajima's D among populations. My VCF file contains information on individuals from four populations.
I imported my VCF file using readData. Due to the large size of the full VCF file, I had to split it by chromosome. As a result, all the output statistics are provided for each chromosome separately. I can also perform pairwise comparisons between populations, but these statistics are also chromosome-specific.
I am wondering how I can process these results to obtain overall statistics for each population, instead of chromosome-wise statistics for each population.
Thank you in advance.
Cheers,
Yixuan
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You can export the relevant information into a csv for each chromosome, then merge them into a single dataset where you can calculate genome-wide values.
Thank you very much!