Identifying variants in mitochondria normal/tumor pairs

[ramiro2k]

Hello,

We are looking for interesting variants in a mitochondrial genome sequenced from cancer tumor/nearby-normal pairs. Each mitochondrial genome can be considered a population of haploids so we are looking for a tool to help us identify variants. We were using mutect but it only works with diploid genomes. Any suggestions on what software to use to help us identify variants in mitochondrial genomes normal/tumor pairs??

Thanks in advance,
Ramiro