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KCCG / mity

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data
MIT License
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Non-model references? #54

Closed chicopollo closed 1 month ago

chicopollo commented 2 months ago

Hi, I am very interested in applying the mity pipeline to non-model organisms for which there are annotated mitochondrial genomes. Is it possible to pass an argument to mity providing my own reference files?

It would be greatly appreciated

drmjc commented 1 month ago

Hi, mity has the functionality to support different references, but not to provide a custom one. if you know python it would be pretty easy to add a new one and to put the custom fasta file in the right location. However, because mity adds lots of human annotations, I think you'd be better off running freebayes using the sensitive parameters that are coded into the app.