The Ensembl Variant Effect Predictor.

doi:10.1186/S13059-016-0974-4

Open AccessJournal ArticleDOI

The Ensembl Variant Effect Predictor.

William M. McLaren, +7 more

- 06 Jun 2016 -

Genome Biology

- Vol. 17, Iss: 1, pp 122-122

TLDR

The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.

Abstract:

The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.

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The Immune Landscape of Cancer

Vesteinn Thorsson, +50 more

- 17 Apr 2018 -

Immunity

TL;DR: An extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA identifies six immune subtypes that encompass multiple cancer types and are hypothesized to define immune response patterns impacting prognosis.

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Journal ArticleDOI

Twelve years of SAMtools and BCFtools.

Petr Danecek, +10 more

- 01 Feb 2021 -

GigaScience

TL;DR: The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines and are freely available on GitHub under the permissive MIT licence, free for both noncommercial and commercial use.

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Journal ArticleDOI

Functional mapping and annotation of genetic associations with FUMA

Kyoko Watanabe, +5 more

- 28 Nov 2017 -

Nature Communications

TL;DR: FUMA is a web-based bioinformatics tool that uses a combination of positional, eQTL and chromatin interaction mapping to prioritize likely causal variants and genes and directly aid in generating hypotheses that are testable in functional experiments aimed at proving causal relations.

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Journal ArticleDOI

CADD: predicting the deleteriousness of variants throughout the human genome.

Philipp Rentzsch, +5 more

- 08 Jan 2019 -

Nucleic Acids Research

TL;DR: The latest updates to CADD are reviewed, including the most recent version, 1.4, which supports the human genome build GRCh38, and also present updates to the website that include simplified variant lookup, extended documentation, an Application Program Interface and improved mechanisms for integrating CADD scores into other tools or applications.

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Journal ArticleDOI

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

Janet Piñero, +8 more

- 04 Jan 2017 -

Nucleic Acids Research

TL;DR: DisGeNET is a versatile platform that can be used for different research purposes including the investigation of the molecular underpinnings of specific human diseases and their comorbidities, the analysis of the properties of disease genes, the generation of hypothesis on drug therapeutic action and drug adverse effects, the validation of computationally predicted disease genes and the evaluation of text-mining methods performance.

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References

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Open Access

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Journal ArticleDOI

An integrated encyclopedia of DNA elements in the human genome

Principal investigators, +3 more

- 06 Sep 2012 -

Nature

TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.

...read moreread less

Journal ArticleDOI

A method and server for predicting damaging missense mutations.

Ivan Adzhubei, +7 more

- 01 Apr 2010 -

Nature Methods

TL;DR: A new method and the corresponding software tool, PolyPhen-2, which is different from the early tool polyPhen1 in the set of predictive features, alignment pipeline, and the method of classification is presented and performance, as presented by its receiver operating characteristic curves, was consistently superior.

...read moreread less

Journal ArticleDOI

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

Kai Wang, +2 more

- 01 Sep 2010 -

Nucleic Acids Research

TL;DR: The ANNOVAR tool to annotate single nucleotide variants and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP is developed.

...read moreread less

Journal Article

An integrated encyclopedia of DNA elements in the human genome.

ENCODEConsortium

- 01 Jan 2012 -

Nature

TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.

...read moreread less

Journal ArticleDOI

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

Pablo Cingolani, +8 more

- 01 Apr 2012 -

Fly

TL;DR: It appears that the 5′ and 3′ UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus.

...read moreread less