Proposed workflows for highly sensitive and specific indel detection from PGM data. BAM files were generated by read alignment of PGM sequencing outputs using either TMAP-TS3.4 (blue) or BWA (red). SAMtools was used to call indels. This was followed by a post-indel calling filtering using QDth and VARWth. An independent confirmation of called indel was performed using Sanger sequencing. The numbers of indels called by each step were specified.