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> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended
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I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K).
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you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator :
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cross posted in bioconductor.
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By following above approach I got this
![enter image description here][1]
[1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
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I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
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