Alternative genetic codes in bcftools csq for mitochondrial variant annotation

[etwatson]

Hello,

I’ve been using snpEff for variant effect prediction and find it very useful. However, I have noticed some instances of multi-nucleotide polymorphisms that nullify effect predictions based on single nucleotides - so I have become very interested in using bcftools csq in order to perform this analysis in a haplotype-aware manner.

I frequently analyze mitochondrial variants, which often require the use of alternative genetic codes. Fun mitochondria in fungi that contain mobile introns! From what I can tell, bcftools csq does not currently support specifying different genetic codes for annotation.

Would it be possible to add an option to allow users to specify an alternative genetic code when running bcftools csq? This would be particularly helpful for those working with mitochondrial genomes, where the standard nuclear genetic code does not apply.

If there is already a workaround for this, I would appreciate any guidance. Otherwise, I’d love to hear if this could be considered as a feature request.

Thanks for your time, and I appreciate all the work that goes into maintaining bcftools!