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 variant reinterpretation given the constantly updated information, require robust data management systems and organized approaches. In this paper, we present iVar: a freely available and highly customizable tool with a user-friendly web interface. It represents a platform for the unified management of variants identified by different sequencing technologies. iVar accepts variant call format (VCF) files and text annotation files and elaborates them, optimizing data organization and avoiding redundancies. Updated annotations can be periodically re-uploaded and associated with variants as historically tracked attributes, i.e., modifications can be recorded whenever an updated value is imported, thus keeping track of all changes. Data can be visualized through variant-centered and sample-centered interfaces. A customizable search function can be exploited to periodically check if pathogenicity-related data of a variant has 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 carrying a specific variant. We tested iVar by uploading 4171 VCF files and 1463 annotation files, obtaining a database of 4166 samples and 22,569 unique variants. iVar has proven to be a useful tool with good performance in terms of collecting and managing data from a medium-throughput laboratory.

Sequencing during Times of Change: Evaluating SARS-CoV-2 Clinical Samples during the Transition from the Delta to Omicron Wave

“…In addition to the potential for recombination events, we also evaluated potential associations between identified mutations and the severity of disease in the patient. Studies suggested that missense mutations could be related to the virus’s ongoing adaptation, reduced symptoms, or disease severity, along with changes in other characteristics such as transmission rates [ 28 , 29 ]. Therefore, we examined the impacts of frequencies of silent and missense mutations on four groups of variants and patient outcomes: Omicron-ICU (group A), Omicron-not-ICU (group B), Delta-ICU (group C), and Delta-not-ICU (group D) ( Supplemental Figure S3 , Supplemental Table S4 ).…”

“…Bwa-mem [ 27 ] was used for paired-end reads mapping to the Wuhan-Hu-1 reference genome (NCBI RefSeq accession NC_045512.2). Primer trimming was performed with iVar [ 28 ] using bed files specific to Artic V4.1 or Varskip2, respectively. Trimmed bam files were then realigned, deduplicated for final coverage evaluation, and called for variants using “ivar variants −q 20 −t 0.3 −m 30”.…”

SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay

“…Libraries were sequenced on the Illumina NextSeq1000 (2 × 109). Sequencing reads adapter sequences were trimmed using trim-galore, aligned to the Wuhan1 reference genome (MN908947.3) using the Burrows-Wheeler aligner, BWA-MEM version 0.7.17-r1188 [15], and had their primer sequences trimmed using iVAR version 1.3.1 [16]. Pangolin version 3.1.14 [17], with its pangolin-designation libraries up to date at the time of analysis, was used to assign lineage designations.…”

Genome sequencing and analysis of the raccoon variant rabies lyssaviruses directly from clinical samples, Connecticut, 2017–2019

“…Trimmed reads were mapped to a known reference rabies genome sequence using the Bowtie2 assembler version 2.3.4.3 (http://bowtie-bio.sourceforge.net/bowtie2). The consensus genome was called using iVar consensus version 1.2.3 (22). The complete coding genome sequences of the RRVs sequenced in this study have been deposited in the GenBank under Accession Numbers ON986428-30, ON986432-41, ON986443-55, ON986457, ON986467-69, ON986471-72, ON986474, ON986476-77, and ON986479-80.…”