VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data

Even though next-generation sequencing (NGS) has become an invaluable tool in molecular biology, several laboratories with NGS facilities lack trained Bioinformaticians for data analysis. Here, focusing on the variant detection application of NGS analysis, we have developed a fully automated pipeline, namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI), which detects and annotates single nucleotide polymorphisms and insertions/deletions from raw sequence reads. VDAP-GUI consolidates several proven methods in each step such as quality control, trimming, mapping, variant detection and annotation. It supports multiple NGS platforms and has four methodological choices for variant detection. Further, it can re-analyze existing data with alternate thresholds and generates easily interpretable reports in html and tab-delimited formats. Using VDAP-GUI, we have analyzed a publically available human whole-exome sequence dataset. VDAP-GUI is developed using Perl/Tk programming, and is available for free download and use at http://sourceforge.net/projects/vdapgui/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13205-016-0382-1) contains supplementary material, which is available to authorized users.