Visualizing genome data
The Integrated Genomics Viewer (IGV) was developed as a tool by the Broad Institute in 2011 to visualize next generation sequencing data. While IGV can assist mutation discovery, its user interface limits the efficiency of scientists parsing through substantial amounts of data. The goal of this project was to optimize an IGV companion tool developed by a previous Helios Scholar that allowed users to input a list of variant coordinates in several different formats and obtain screenshots of variants in IGV. This project allows users to now input lists of samples and genes, creating summary tables for the user that table provides useful information for a scientist attempting to study harmful mutations. The project added a command-line implementation tailored to improve efficiency and work alongside the TGen bioinformatics pipeline for analyzing genomic data. The project was also updated by implementing a rudimentary form of variant discovery. The software accepts user-input variant call format (VCF) files and a list of genes and searches for variants within the genes provided in the VCF files. The application filters VCF files, only producing snapshots when the variant is prevalent in a majority of reads in the aligned data. The tool offers improved options for scientists to pursue analysis of variants and discover relevant mutations that may cause disease either through prior knowledge (variant coordinate list is provided) or through an agnostic approach (with only a gene list is provided).