DNASTAR’s SeqMan NGen application offers advanced SNP options for users to customize their NGS assembly parameters. Ion Torrent data is known to have an increased error rate in homopolymeric runs, reducing the accuracy of base calling of heterozygous insertions or deletions in these regions. The ability to specify automatic removal of heterozygous indels within Seqman NGen addresses this concern and produces the most accurate assembly and variant calling for Ion Torrent data.
Comparative studies of Ion Torrent data with and without heterozygous indel removal illustrate that removal of heterozygous indels greatly decreases the false discovery rate of these assemblies.
For more information, please read our white paper SeqMan NGen Assembly of Ion Torrent Exome Data With and Without Heterozygous Indel Removal: a Comparison Using NA12878 Reference Materials