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Old 08-20-2013, 11:06 AM   #1
Genomics101
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Location: Maryland, USA

Join Date: May 2012
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Default How to calculate nucleotide diversity (pi and theta) using NextGen Data?

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!
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