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A Pipeline for Variant Calling in Tumor Panels Using Amplicon Sequencing Data

Analysis of raw data generated from Next Generation Sequencing (NGS) equipments is critical in detection of pathogenic and non-pathogenic variants. Illumina MiSeq for instance has a software called Miseq-Reporter [1] which performs the analysis of the sequencing raw data. Miseq-Reporter was built to handle several workflows along with amplicon workflow such as assembly and enrichment workflows. Moreover, many procedures, such as removing non-unique alignments and remov-ing reads with N bases, need to be applicable for the analysis. There are also other pipelines available but none meets all the following features: oriented to the analysis of NGS amplicon data, uses a range of flexible procedures, and is academically free. In this paper, we report the development and implementation of an in-house pipeline which is oriented to the analysis of NGS amplicon data, applies a range of parameterized procedures that are needed to be applicable in the variant-calling analysis using amplicon data, and is academically free.