Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes: Fig. 1.

(2015) Hue Vuong et al.   BIOINFORMATICS

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

(2015) C. Dong et al.   HUMAN MOLECULAR GENETICS

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data

(2014) Hao Hu et al.   NATURE BIOTECHNOLOGY

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Choice of transcripts and software has a large effect on variant annotation

(2014) Davis J McCarthy et al.   Genome Medicine

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

(2014) Catherine A Brownstein et al.   GENOME BIOLOGY

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

(2013) Min Zhao et al.   BMC BIOINFORMATICS

VAAST 2.0: Improved Variant Classification and Disease-Gene Identification Using a Conservation-Controlled Amino Acid Substitution Matrix

(2013) Hao Hu et al.   GENETIC EPIDEMIOLOGY

dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations

(2013) Xiaoming Liu et al.   HUMAN MUTATION

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Whole-Exome Sequencing to Identify a Novel LMNA Gene Mutation Associated with Inherited Cardiac Conduction Disease

(2013) Chun-Chi Lai et al.   PLoS One

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

(2013) Umadevi Paila et al.   PLoS Computational Biology

Using ERDS to Infer Copy-Number Variants in High-Coverage Genomes

(2012) Mingfu Zhu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

(2012) Lukas Habegger et al.   BIOINFORMATICS

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

(2012) H. Li   BIOINFORMATICS

AnnTools: a comprehensive and versatile annotation toolkit for genomic variants

(2012) Vladimir Makarov et al.   BIOINFORMATICS

Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation

(2012) Jacob J. Michaelson et al.   CELL

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

wANNOVAR: annotating genetic variants for personal genomes via the web

(2012) Xiao Chang et al.   JOURNAL OF MEDICAL GENETICS

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

(2012) Wenqing Fu et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing

(2012) I. Medina et al.   NUCLEIC ACIDS RESEARCH

Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress

(2012) Gholson J Lyon et al.   Genome Medicine

Exome Sequencing Identifies a DYNC1H1 Mutation in a Large Pedigree with Dominant Axonal Charcot-Marie-Tooth Disease

(2011) Michael N. Weedon et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Increased exonic de novo mutation rate in individuals with schizophrenia

(2011) Simon L Girard et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

(2011) G. De Baets et al.   NUCLEIC ACIDS RESEARCH

Regenerative phenotype in mice with a point mutation in transforming growth factor   type I receptor (TGFBR1)

(2011) J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

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

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

dbSNP in the detail and copy number complexities

(2009) Ian N.M. Day   HUMAN MUTATION

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY