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How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools

. I am using mtDNA PacBio data to calculate nucleotide diversity. For my analysis, I have been utilizing bioinformatics tools on a Linux platform. Initially, I tried using Samtools and BCFtools, followed by running a script in Python (PyCharm) to measure nucleotide diversity, but I was unsuccessful. Suggest me some tools for these calculations. I humbly request your guidance from the beginning. Could please someone help me?

Thank you for your assistance.

Best regards,

nucleotidediversity mtdna pacbio
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written by hashim.rana11 • hashim.rana11

Initially, I tried using Samtools and BCFtools, followed by running a script in Python (PyCharm) to measure nucleotide diversitynucleotide_diversity_screenshot

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written by hashim.rana11 • hashim.rana11

1 answer

Variants should be called using a specialized mitochondrial variant caller, e.g.: GATK Mutect2 CallMt

Then, pi, Tajima's D, and other statistics could be estimated with vcftools from the vcf files, here is a tutorial.

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written by Michael Dondrup Michael Dondrup

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