re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files

Introduction

Recent achievements in high-throughput sequencing technologies (Goodwin, McPherson & McCombie, 2016; van Dijk et al., 2018) have led to the generation of massive amounts of genomic data (Gao et al., 2019; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, 2020) available for the research community. Many omics databases have been developed and have collected freely accessible datasets (Molkenov et al., 2019; Rigden & Fernández, 2020) for analysis by the bioinformatics community. Modern bioinformatics tools and methods are in high demand for analyzing and interpreting the big omics data generated by the different types of multi-omics platforms available. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) (Danecek et al., 2011) is a tab-delimited text file format that is often used in bioinformatics to store genomic variants. A VCF file consists of the header, including meta-information lines and field definition lines (column names), and the body (data section). An arbitrary number of meta-information lines start with ’##’ and provide a description of the VCF file. The body of the file consists of eight mandatory columns: chromosome (CHROM), starting position of a variant (POS), variant identifiers (ID), the reference allele (REF), a list of alternate alleles (ALT), a PHRED-scaled quality score (QUAL), filter information regarding variant validity (FILTER), and annotation information (INFO). Additional columns describing samples can also be added. Each row of the file describes specific genomic variants (SNVs, INDELs, CNVs, and other structural variants) at the given chromosome and genomic position.

VCF files often store information about numerous samples and can therefore reach huge sizes–gigabytes, or sometimes terabytes. This creates an issue for the readability of VCF files and further analysis for non-programmers, as manual data extraction and analysis using Microsoft Excel or other table processing software may not be possible due to the RAM capacity limitation of standard computers. We introduce re-Searcher, bioinformatics tool specifically developed for simplified mining and analysis of big-size VCF files. We developed a multi-platform user-friendly graphical user interface (GUI) tool for offline access, while re-Searcher web application can be used online via web browser. re-Searcher has been developed for the broader biomedical community and solves the problem of working and analyzing genomics data stored in...