MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided.
This mitosalt version can:
download-mitosalt-db.sh -h [human_genome_url, blank for custom hg19 genome]download-mitosalt-db.sh -m [mouse_genome_url, blank for custom GRCm38.p6 genome]download-mitosalt-db.sh -h [human_genome_url, blank for custom hg19 genome] -m [mouse_genome_url, blank for custom GRCm38.p6 genome]export MITOSALTDATA=/path/to/mitosalt/genomedata$CONDA_PREFIX/share/mitosalt-1.1.1-0/