Multiplex Y-STRs analysis using the ion torrent personal genome machine (PGM)

•Multiplex Y-STR genotyping of 13 Y-STRs is feasible by MPS.•Only one allele of DYS390 showed inconsistent results between CE and MPS typing method because of 4bp deletions upstream of the core repeat unit.•Several new alleles with identical lengths but with different sequences were observed in DYS389 II, DYS390, DYS437, DYS438, DYS448 and DYS635.•Two DYS448 dropouts were observed in a total of 42 samples detected by both CE and MPS methods.