Mutserve2 is a variant caller for the mitochondrial genome to detect homoplasmic and heteroplasmic sites in sequence data.
We recommend to use our Nextflow DSL2 pipeline for mtDNA-Server 2 which includes mutserve2.
Mutserve requires sorted and indexed CRAM/BAM files as an input.
curl -sL mutserve.vercel.app | bash
./mutserve
Full documentation for mutserve can be found here.
The focus of mutserve is currenly on SNP calling and not on indels.
See here.
Weissensteiner H, Forer L, Fendt L, Kheirkhah A, Salas A, Kronenberg F, Schoenherr S. 2021. Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res. 31: 309-316
Weissensteiner H, Forer L, Fuchsberger C, Schöpf B, Kloss-Brandstätter A, Specht G, Kronenberg F, Schönherr S. 2016. mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud. Nucleic Acids Res 44: W64–9.