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SNP/SNV annotation software tools | Whole-exome sequencing data analysis

Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects.Source text:(Jager et al., 2014) Jannovar: a java…
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Vcfanno
Web

Vcfanno

Simplifies the annotation of genetic variants in VCF format. Vcfanno can…

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…

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COPE-PCG
Web
Desktop

COPE-PCG Context-Oriented Predictor for variant Effect - Protein-Coding Genes

Predicts variant effects on protein-coding genes in a context-sensitive…

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,…

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cnvScan
Desktop

cnvScan

A tool to improve the clinical utility of computational CNV prediction in exome…

A tool to improve the clinical utility of computational CNV prediction in exome data. cnvScan can accept input from any CNV prediction program. cnvScan consists of two steps: CNV screening and CNV…

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TREAT
Desktop

TREAT

A Targeted RE-sequencing Annotation Tool that offers a comprehensive, open…

A Targeted RE-sequencing Annotation Tool that offers a comprehensive, open framework, end-to-end solution for analyzing and interpreting targeted re-sequencing data.

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DaMold
Web

DaMold

Permits to filter, annotate, cross-link, and visualize Next Generation…

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…

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FamAnn
Desktop

FamAnn

An automated variant annotation pipeline designed for facilitating target…

An automated variant annotation pipeline designed for facilitating target discovery for family-based sequencing studies.

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PriVar
Desktop

PriVar

A cross-platform Java application toolkit to prioritize variants (SNVs and…

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…

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Exomiser
Web

Exomiser

A Java program that functionally annotates variants from whole-exome sequencing…

A Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF file.

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OVarCall
Desktop

OVarCall

Allows detection of somatic mutations with low allele frequencies from exome…

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…

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CanvasDB
Desktop

CanvasDB

An infrastructure for management and analysis of genetic variants from…

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…

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VaRank
Desktop

VaRank

A simple and powerful tool designed for variant ranking from next generation…

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…

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Jannovar
Desktop

Jannovar

A stand-alone Java application as well as a Java library designed to be used in…

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…

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Pynnotator
Desktop

Pynnotator

Annotates Variant Call Formats (VCFs) generated from build GRCh37. Pynnotator…

Annotates Variant Call Formats (VCFs) generated from build GRCh37. Pynnotator was designed to annotate VCF files (Exomes or Genomes) from patients with Mendelian Disorders. The software uses…

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Vanno
Web

Vanno

A Web-based application for in-depth analysis and rapid evaluation of…

A Web-based application for in-depth analysis and rapid evaluation of disease-causative genome sequence alterations. Vanno integrates information from biomedical databases, functional predictions…

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