Dec 17, 2015

BrowseVCF: a web-based application and workflow to quickly prioritise disease-causative variants in VCF files.

BioRxiv : the Preprint Server for Biology
Silvia SalatinoStefano Lise

Abstract

As sequencing cost continues to decrease with fast advancing Next Generation Sequencing (NGS) technologies, variant discovery is becoming a more affordable and popular analysis method among research laboratories. Following variant calling and annotation, accurate variant filtering is a crucial step to extract meaningful biological information from sequencing data and to investigate disease etiology. However, the standard variant call file format (VCF) used to store this valuable information is not easy to handle without bioinformatics skills, thus preventing investigators from directly analysing their data. Here, we present BrowseVCF, an easy-to-use stand-alone software that enables researchers to browse, query and filter millions of variants in a few seconds. Top features include the possibility to store intermediate search results, to query user-defined gene lists, to group samples for family or tumour/normal studies, to download a report of the filters applied, and to export the filtered variants in spreadsheet format. Additionally, BrowseVCF is suitable for any DNA variant analysis (exome, whole-genome and targeted sequencing), can be used also for non-diploid genomes, and is able to discriminate between Single Nucleotide P...Continue Reading

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Mentioned in this Paper

Computer Software
Gene Polymorphism
Study
Genome
Genes
Permissiveness, Biological Function
Research Personnel
Neoplasms
Gene Deletion
Nucleic Acid Sequencing

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