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Mitochondrial Genome Variant Calling and Annotation Tools

Hi,

I have Illumina data generated from Mitochondrial DNA by amplicon approach. I need to perform variant calling and annotation. Custom annotations like population allele frequency, haplogroup identification, etc also need to be done. For this I need an end-to-end pipeline like MToolBox. However this tools is very old and no longer supported.

Are there any other alternative pipelines available that can directly take fastq files from amplicon sequencing. I saw tools like Mity and mitopy. But those are developed for whole genome data and requires a WGS aligned BAM.

Please help me with some suggestions on how to proceed.

Thanks

illumina amplicon mitochondria
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by adarsh • adarsh

1 answer

. For this I need an end-to-end pipeline like MToolBox. However this tools is very old and no longer supported.

https://github.com/genepi/mtdna-server-2

mtDNA-Server 2 is a Nextflow DSL2 pipeline to accurately detect heteroplasmic and homoplasmic variants in mitochondrial (mtDNA) genomes, details can be found in our NAR publication.

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written by Pierre Lindenbaum Pierre Lindenbaum

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