MHTyper: a microhaplotype allele-calling pipeline for use with next generation sequencing data

Microhaplotypes have been reported for applications in different aspects of human forensics. Next generation sequencing (NGS) possesses several advantages in microhaplotype genotyping. Large amounts of NGS-based microhaplotype data has been accumulated, and bioinformatic software designed for microhaplotype NGS data analysis is in urgent need. In this work, we introduced MHTyper, a Linux/Unix pipeline designed for efficient microhaplotype allele-calling and sequencing depth statistics. We developed an NGS-based 30-plex microhaplotype panel and used MHTyper to analyse the data produced. The allele-calling accuracy of MHTyper was evaluated by manually comparing the MHTyper-reported genotypes with those visualized, along with the well-accepted bioinformatic software Integrative Genomics Viewer. No discordance was observed in all 150 pairs for comparison. These data supported that MHTyper could provide an efficient tool for NGS-based forensic microhaplotype data analysis.