Mutserve2 is a variant caller for the mitochondrial genome to detect homoplasmic and heteroplasmic sites in sequence data.
Mutserve Variant Calling:
mutserve call
--reference rCRS.fasta
--output HG00096.vcf.gz
--threads 4
*.bam
The full list of parameters is available here.
Mutserve Variant Annotation:
mutserve annotate
--input variantfile.txt
--annotation rCRS_annotation_2020-08-20.txt
--output AnnotatedVariants.txt
rCRS.fasta, rCRS_annotation_2020-08-20.txt, and rCRS_annotation_descriptions.md are available in the Mutserve2 repository ($MUTSERVE_DATA/).