Amplicon Indel Hunter
Amplicon Indel Hunter (AIH) is a novel reference-independent algorithm for detecting large indels in paired-end amplicon-based targeted sequencing data.
The AIH method is described in detail in:
Kadri et al. (2015) Amplicon Indel Hunter: A Novel Bioinformatics Tool to Detect Large Somatic Insertion/Deletion Mutations in Amplicon-Based NGS Data
Link to the software can be found bellow.