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.
Simplifies the annotation of genetic variants in VCF format. Vcfanno can extract and summarize multiple attributes from one or more annotation files and append the resulting annotations to the INFO field of the original VCF file. Vcfanno also integrates the lua scripting language so that users can easily develop custom annotations and metrics. It represents a substantial improvement over existing methods, enabling rapid annotation of whole-genome and whole-exome datasets and provides substantial analytical power to studies of disease, population genetics, and evolution.
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.
Predicts variant effects on protein-coding genes in a context-sensitive approach. COPE-PCG is part of COPE, a framework for predicting the effects of variants through a context-sensitive, gene-centric approach.
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 cross-platform Java application toolkit to prioritize variants (SNVs and InDels) from exome or whole genome sequencing data by using different filtering strategies and information of external databases. PriVar contains four modules: annotation, quality control, candidate gene identification and prediction of functional impact of variants.
Facilitates disease variants or genes discovery for family-based sequencing studies. FamAnn is an automated variant annotation pipeline that selects and annotates variants segregating in each family and shared across families. The software can be applied to all types of sequencing data, such as whole-exome sequencing, genome sequencing or targeted resequencing. It can be applied to variant discovery for Mendelian or complex disease studies.
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.
Enables visualization and analysis of genetic alteration profiles. Vanno is a variant annotation tool that provides an interface to annotate and examine genetic variants through. The software allows functional analysis of genomic variants at both the gene level and protein domain level. It supports a wide variety of different variant calling formats and almost all commercially available sequencing gene and exome panels. Vanno can assist users in translating cancer genomic data into biological insights and potential clinical applications.
Permits to filter, annotate, cross-link, and visualize Next Generation Sequencing (NGS), Sanger, and hotspot variants. DaMold can predict the effect of each variant, such as codon and amino acid change. It permits (1) to filter variants, (2) to predict variant effect, (3) functional and clinical annotation, and (4) to create a variant summary table. It enables users to analyze tens to thousands of variants from sequencing experiments (NGS and Sanger).
Improves the clinical utility of computational copy number variants (CNVs) prediction. cnvScan enables users to evaluate CNVs predicted from any program. It also provides robust CNV quality assessment to reduce the false positive count. It enables the identification of three high-quality rare CNVs in two families. As input, this method can use a CNV results file from any prediction program.
Allows detection of somatic mutations with low allele frequencies from exome sequence data. OVarCall is a Bayesian hierarchical method which uses the information of overlapping paired-end reads for detecting low allele frequency somatic single nucleotide variants (SNVs). The method was evaluated using two types of tumor allele frequency (10% and 1%), four pairs of average and variance of DNA fragment size, and three pairs of average and variance of depth around the true SNVs or error prone sites.
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.
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.
Aims to assist researchers in the investigation of next-generation sequencing (NGS) data. MutationDistiller contains an interactive interface and is designed to be customizable by users. The tool’s interface allows researchers to visualize specific hidden sections with a simple click, facilitating the personalization. It offers a solution for running quick analysis or for creating an optimized study.
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.