The advent of Next Generation Sequencing has revolutionized the research in biological sciences in general and forensics particularly. Next generation sequencing (NGS) helps in detection of mitochondrial DNA (mtDNA) properties like heteroplasmy (i.e. intra-individual sequence variation) to a much deeper level than Sanger Sequencing. This creates a need for development of efficient and reliable pipelines for detection of heteroplasmy. While various pipelines for estimating heteroplasmy exist but these pipelines have built in issues of access, usability and confidentiality of data. Here we present mtVarCaller, an efficient pipeline for heteroplasmy detection that is easy to use and can reliably calculate heterplasmy from BAM files of mtDNA.

The pipeline operates only on Linux and is developed using pysam module of Python. The mtVarCaller workflow includes reading the BAM file, filtering the BAM file, comparison with Revised Cambridge Reference Sequence and calculation of heteroplasmy. We have also applied a new filter for estimating heteroplasmy that is not yet been available in any of the previously developed pipelines and servers. We have tested the pipeline on 5 samples and found reliable in terms of sensitivity and specificity. The pipeline will be freely available at