An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). Using a desktop computer, ANNOVAR requires ∼4 min to perform gene-based annotation and ∼15 min to perform variants reduction on 4.7 million variants, making it practical to handle hundreds of human genomes in a day.
Enables prioritization of genes and variants in next-generation sequencing (NGS) projects for novel disease-gene discovery or differential diagnostics of Mendelian disease. Exomiser is a suite that contains several different methods for variant prioritization, based on protein-protein interactions and/or phenotype comparisons between a patient and existing human disease databases and model organisms. It provides methods using clinical data, model organism phenotype data, as well as random-walk analysis of protein interactome data to perform prioritization.
A web app for detecting and analyzing structural variants from a de novo genome assembly aligned to a reference genome. Assemblytics analyzes the alignments from MUMmer’s nucmer program to identify high-confidence structural variants in each sequence (contig) in the sample relative to a reference or another de novo assembly. It incorporates a unique anchor filtering approach to increase robustness to repetitive elements, and identifies six classes of variants based on their distinct alignment signatures. Assemblytics can be applied both to comparing aberrant genomes, such as human cancers, to a reference, or to identify differences between related species. Multiple interactive visualizations enable in-depth explorations of the genomic distributions of variants.
A simple and powerful tool designed for variant ranking from next generation sequencing data. VaRank provides a comprehensive workflow for annotating and ranking SNVs and indels. Four modules create the strength of this workflow: (i) Variant call quality summary (total and variant depth of coverage, phred like information), to filter out false positive calls, (ii) Alamut Batch or SnpEff variant annotations, to integrate genetic and predictive information (functional impact, putative effects in the protein coding regions, population frequency...) from different sources, using HGVS nomenclature, (iii) Barcode representing the presence/absence of variants (with homozygote/heterozygote status), to search for recurrence between families or group of individuals, and (iv) Prioritization score, to rank variants according to their predicted pathogenic status. VaRank results aims at reducing the daily work of clinical geneticists and molecular biologists and will help to accelerate the progress in identifying disease causing variants.
Allows users to investigate functional variants. SinBaD is a web application that supplies a quantitative measure for estimate the functionality of a mutation including intron and promoter regions. It can be used for picking candidate variants in a specific gene and aims to provide an enhanced picture of variants in coding regions as well as providing functional variant detection in non-coding regions.
A stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar is freely available under the BSD2 license.
An infrastructure for management and analysis of genetic variants from massively parallel sequencing (MPS) projects. The system stores SNP and indel calls in a local database, designed to handle very large datasets, to allow for rapid analysis using simple commands in R. Functional annotations are included in the system, making it suitable for direct identification of disease-causing mutations in human exome- (WES) or whole-genome sequencing (WGS) projects.