VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database

Advancements in Next-Generation Sequencing

(2016) Shawn E. Levy et al.   Annual Review of Genomics and Human Genetics

A homozygous nonsense variant inIFT52is associated with a human skeletal ciliopathy

(2016) K. M. Girisha et al.   CLINICAL GENETICS

Human genetic variation database, a reference database of genetic variations in the Japanese population

(2016) Koichiro Higasa et al.   JOURNAL OF HUMAN GENETICS

ExAC project pins down rare gene variants

(2016)   NATURE

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data

(2016) Ramesh Menon et al.   3 Biotech

VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data

(2016) Ramesh Menon et al.   3 Biotech

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The human gene damage index as a gene-level approach to prioritizing exome variants

(2015) Yuval Itan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders

(2014) Margherita Mutarelli et al.   BMC GENOMICS

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

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

(2014) Martin Kircher et al.   NATURE GENETICS

STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

(2014) Konrad J. Karczewski et al.   PLoS One

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

(2013) Mattia D'Antonio et al.   BMC BIOINFORMATICS

Evaluating empirical bounds on complex disease genetic architecture

(2013) Vineeta Agarwala et al.   NATURE GENETICS

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

(2013) Umadevi Paila et al.   PLoS Computational Biology

Detection and Impact of Rare Regulatory Variants in Human Disease

(2013) Xin Li et al.   Frontiers in Genetics

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

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Disease gene identification strategies for exome sequencing

(2012) Christian Gilissen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

Detecting and annotating genetic variations using the HugeSeq pipeline

(2012) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data

(2012) Maria Fischer et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Xiaoming Liu et al.   HUMAN MUTATION

Unlocking Mendelian disease using exome sequencing

(2011) Christian Gilissen et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

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

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

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

(2009) Murim Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA