The Exome Aggregation ConsortiumThe Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a wide variety of large-scale sequencing projects. The data set provided on this website spans 60,706 unrelated individuals sequenced as part of various disease-specific and population genetic studies.
The NHLBI GO Exome Sequencing ProjectThe goal of the NHLBI GO Exome Sequencing Project (ESP) is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to share these datasets and findings with the scientific community to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders.
UK10KMany hundreds of genes that are involved in causing disease have already been identified, but it is believed that many more remain to be discovered. The UK10K project aims to help uncover them by studying the genetic code of 10,000 people in much finer detail than ever before.
The 1000 GenomesThe 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data.
dbSNPEstablished by The National Center for Biotechnology Information, the dbSNP database is to serve as a central repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.
FamSeqFamSeq is a family-based variant calling program, which builds on Bayesian networks and the Markov chain Monte Carlo algorithm.
TrioDeNovo TrioDeNovo can be applied to both whole exome sequencing and whole genome sequencing data, which can be equipped with DNMFilter to detect mutations in trios.
DNMFilter DNMFilter is a gradient boosting-based approach for filtering DNMs identified in parent-offspring trios, which takes BAM format files as input. It classifies candidates as true or false de novo mutations with the employed machine learning approach.
Scalpel Scalpel is developed to detect de novo likely gene-disrupting transmitted Indels within exome-capture data on the basis of localized assembly.
PolyMutt PolyMutt is a standalone software package for polymorphism and mutation detection which accepts VCF or GLF files as input. It can be applied to call SNPs and Indel.
DeNovoGear DeNovoGear is based on human whole-genome sequencing data or exome sequencing data to produce a set of predicted de novo Indels.
mirTrios mirTrios is a web server developed to identify de novo SNPs/Indels and rare inherited mutations using trio-based or family-based VCF results based on NGS in sporadic diseases.
ANNOVARANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes.
wANNOVARwANNOVAR provides easy and intuitive web-based access to the most popular functionalities of the ANNOVAR software.
dbNSFPdbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome.
snpEFFSnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).
SeqAntSeqAnt annotates single base mutations, insertions, and deletions sequenced on any platform.
VATA computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.
VAASTVAAST (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences.
HPOThe Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect.
OMIMOnline Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily.
ClinvarClinVar provides a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence.
MGIMGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.
NHGRI-EBI GWAS CatalogThe NHGRI-EBI Catalog of published genome-wide association studies.
NPdenovo A database of de novo mutations in neuropsychiatric disorders including autism spectrum disorders (ASD), intellectual disability (ID), epileptic encephalopathy (EE), schizophrenia (SCZ) and unaffected siblings (Control).