iVar, an interpretation-oriented tool to manage the update and revision
of variant annotation and classification
Abstract
The rapid evolution of Next Generation Sequencing in clinical settings
and the resulting challenge of variants interpretation in the light of
constantly updated information, requires robust data management systems
and organized approaches to variant reinterpretation. In this paper, we
present iVar: a freely available and highly customizable tool provided
with a user-friendly web interface. It represents a platform for the
unified management of variants identified by different sequencing
technologies. iVar accepts, as input, VCF files and text annotation
files and elaborates them, optimizing data organization and avoiding
redundancies. Updated annotations can be periodically re-uploaded and
associated to variants as historicize attributes. Data can be visualized
through variant-centered and sample-centered interfaces. A customizable
search functionality can be exploited to periodically check if
pathogenicity related data of a variant are changed over time. Patient
recontacting ensuing from variant reinterpretation is made easier by
iVar through the effective identification of all patients present in the
database and carrying a specific variant. We tested iVar by uploading
4171 VCF files and 1463 annotation files, obtaining a database of 4166
samples and 22569 unique variants. iVar has proven to be a useful tool
with good performances for collecting and managing data from
medium-throughput