For Ion PGM, we have adopted an optimized pipeline based on TMAP and GATK [20 (link)], the OTG-snpcaller for single nucleotide variant based on a previous study [21 (link)]. Briefly, the raw data from Torrent Suite 4.6 was mapped with TMAP 3.6 (https://github.com/iontorrent/TAMP ) and the duplicates were removed with Remove Duplicates according to the Alignment Score Tag. To reduce the false negative results of single nucleotide variant in a gap site, Alignment Optimize Structure filtering method was incorporated. Then the variant calling was performed with GATK tool. Local mutational hotspot files were included for annotation of the variants identified.
For Ion PGM Dx, the sequence data were processed using Ion Torrent Suite software 4.0 processed on the Torrent Server (Thermo Fisher Scientific).
Sequence alignments for variants with discordant results were manually inspected with the Integrative Genomics Viewer (IGV) 2.3 [22 (link)].
For Ion PGM Dx, the sequence data were processed using Ion Torrent Suite software 4.0 processed on the Torrent Server (Thermo Fisher Scientific).
Sequence alignments for variants with discordant results were manually inspected with the Integrative Genomics Viewer (IGV) 2.3 [22 (link)].
