VariantDB: a flexible annotation and filtering portal for next generation sequencing data

The Sequence Alignment/Map format and SAMtools

2009 • 54,537 citations

Fast and accurate short read alignment with Burrows–Wheeler transform

2009 • 51,582 citations

Gene Ontology: tool for the unification of biology

2000 • 38,297 citations

Cutadapt removes adapter sequences from high-throughput sequencing reads

2011 • 26,936 citations

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

2010 • 24,159 citations

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

2009 • 20,860 citations

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

2010 • 12,455 citations

A framework for variation discovery and genotyping using next-generation DNA sequencing data

2011 • 10,899 citations

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

2012 • 9,612 citations

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

2012 • 7,912 citations

A map of human genome variation from population-scale sequencing

2010 • 7,765 citations

dbSNP: the NCBI database of genetic variation

2001 • 6,995 citations

SIFT: predicting amino acid changes that affect protein function

2003 • 5,952 citations

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

2014 • 5,704 citations

Table S2: Trans-factors and trinucleotide repeat instability Trans-factor

2010 • 5,471 citations

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

2013 • 4,522 citations

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

2010 • 3,462 citations

Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2

2013 • 3,308 citations

Predicting the Functional Effect of Amino Acid Substitutions and Indels

2012 • 2,747 citations

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

2013 • 2,709 citations

Amino Acid Difference Formula to Help Explain Protein Evolution

1974 • 2,255 citations

Detection of nonneutral substitution rates on mammalian phylogenies

2009 • 2,145 citations

Galaxy: A platform for interactive large-scale genome analysis

2005 • 2,026 citations

Targeted capture and massively parallel sequencing of 12 human exomes

2009 • 1,986 citations

The UCSC Genome Browser database: update 2011

2010 • 1,753 citations

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

2010 • 1,637 citations

Exome sequencing as a tool for Mendelian disease gene discovery

2011 • 1,627 citations

Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability

2012 • 1,444 citations

Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists

2010 • 1,434 citations

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

2011 • 1,194 citations

A de novo paradigm for mental retardation

2010 • 827 citations

dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions

2011 • 755 citations

Exome sequencing supports a de novo mutational paradigm for schizophrenia

2011 • 464 citations

The Human Phenotype Ontology

2010 • 352 citations

A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP

2014 • 306 citations

A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases

2012 • 250 citations

Diagnostic Exome Sequencing in Persons With Severe Intellectual Disability

2013 • 212 citations

VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer

2011 • 140 citations

Performance comparison of SNP detection tools with illumina exome sequencing data—an assessment using both family pedigree information and sample-matched SNP array data

2014 • 58 citations

WEP: a high-performance analysis pipeline for whole-exome data

2013 • 55 citations

PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data

2012 • 49 citations

A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies

2014 • 41 citations

Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster

2014 • 37 citations

AnFBN1Deep Intronic Mutation in a Familial Case of Marfan Syndrome: An Explanation for Genetically Unsolved Cases?

2014 • 36 citations

Challenges and opportunities in the investigation of unexplained intellectual disability using family‐based whole‐exome sequencing

2014 • 31 citations

Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease

2012 • 30 citations

VAR-MD: A tool to analyze whole exome-genome variants in small human pedigrees with mendelian inheritance

2012 • 30 citations

Patient experiences with gene panels based on exome sequencing in clinical diagnostics: high acceptance and low distress

2014 • 25 citations

Prioritizing Disease-Linked Variants, Genes, and Pathways with an Interactive Whole-Genome Analysis Pipeline

2014 • 25 citations

Integrating Massively Parallel Sequencing into Diagnostic Workflows and Managing the Annotation and Clinical Interpretation Challenge

2014 • 23 citations

EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics

2012 • 21 citations

Detection and interpretation of genomic structural variation in health and disease

2012 • 15 citations

Localization of the gene for X-linked calvarial hyperostosis to chromosome Xq27.3–Xqter

2013 • 12 citations

FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies

2014 • 8 citations

SNPAAMapper: An efficient genome-wide SNP variant analysis pipeline for next-generation sequencing data

2013 • 7 citations

AnsNGS: An Annotation System to Sequence Variations of Next Generation Sequencing Data for Disease-Related Phenotypes

2013 • 4 citations