Nucleotide diversity calculation using SNP calling or alignment ?

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6.4 years ago

khuang1116 ▴ 10

Hi all,

Currently, I am calculating nucleotide diversity and Tajima`s D for a population of bacterium. I have alignment on hand, but I saw lots of pipeline works on vcf. Do you know which one is better? SNP calling or alignment. Many thanks !!!!!

Best Kun

SNP alignment • 2.3k views

ADD COMMENT • link updated 6.3 years ago by Biostar 20 • written 6.4 years ago by khuang1116 ▴ 10

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what is "Tajima`s" D ?

ADD REPLY • link 6.4 years ago by Pierre Lindenbaum 161k

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Hi pierre. Thank you for reply. For detailed definition of Tajima`s D, please look https://en.wikipedia.org/wiki/Tajima%27s_D

ADD REPLY • link 6.4 years ago by khuang1116 ▴ 10

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