Greetings!
I have a number of annotated VCF files from a population of haploid organisms (malaria parasites), all mapped to the same reference, and I would like to get some numbers on genome-wide nucleotide diversity metrics, pi and theta. Any recommendations on software that can do this?
(I did the analysis myself, so of course of the bam files, FASTQs and everything else).
Thanks!
I have a number of annotated VCF files from a population of haploid organisms (malaria parasites), all mapped to the same reference, and I would like to get some numbers on genome-wide nucleotide diversity metrics, pi and theta. Any recommendations on software that can do this?
(I did the analysis myself, so of course of the bam files, FASTQs and everything else).
Thanks!