we have sequenced mitochondrial DNA of BLOOD and TUMOR from oral cancer patients using Ion PGM platform. The inbuilt variant caller produced separate variant call files for blood and tumor data. Our aim is to identify mitochondrial somatic mutations from patients. I have written a tiny code in R to identify variants which are present in tumor only. But so far I am unable to identify heteroplasmic variants which are present in both blood and tumor, but in different frequency.
Ion reporter does not support mitochondrial workflow so we can not go there. Also I have tried varscan2, but it gives a very large number of false indels.
can anybody please suggest any tool/package/pipeline to solve my problem.