High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

(2022) Jana Ebler et al.   NATURE GENETICS

The sequences of 150,119 genomes in the UK Biobank

(2022) Bjarni V. Halldorsson et al.   NATURE

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

(2021) Daniel Taliun et al.   NATURE

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

(2021) Peter Ebert et al.   SCIENCE

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies

(2021) Xuefang Zhao et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A structural variation reference for medical and population genetics

(2020) Ryan L. Collins et al.   NATURE

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Mapping and characterization of structural variation in 17,795 human genomes

(2020) Haley J. Abel et al.   NATURE

Best practices for benchmarking germline small-variant calls in human genomes

(2019) Peter Krusche et al.   NATURE BIOTECHNOLOGY

ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions

(2019) Egor Dolzhenko et al.   BIOINFORMATICS

An open resource for accurately benchmarking small variant and reference calls

(2019) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

svtools: population-scale analysis of structural variation

(2019) David E Larson et al.   BIOINFORMATICS

Profiling the genome-wide landscape of tandem repeat expansions

(2019) Nima Mousavi et al.   NUCLEIC ACIDS RESEARCH

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

The International Genome Sample Resource (IGSR) collection of open human genomic variation resources

(2019) Susan Fairley et al.   NUCLEIC ACIDS RESEARCH

Accurate, scalable and integrative haplotype estimation

(2019) Olivier Delaneau et al.   Nature Communications

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

(2018) Donna M. Werling et al.   NATURE GENETICS

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

(2018) Allison A. Regier et al.   Nature Communications

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology

(2017) Eugene J. Gardner et al.   GENOME RESEARCH

Parental influence on human germline de novo mutations in 1,548 trios from Iceland

(2017) Hákon Jónsson et al.   NATURE

A recurrence-based approach for validating structural variation using long-read sequencing technology

(2017) Xuefang Zhao et al.   GigaScience

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

(2016) Michael A. Eberle et al.   GENOME RESEARCH

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

Reference-based phasing using the Haplotype Reference Consortium panel

(2016) Po-Ru Loh et al.   NATURE GENETICS

A reference panel of 64,976 haplotypes for genotype imputation

(2016)   NATURE GENETICS

Deep sequencing of 10,000 human genomes

(2016) Amalio Telenti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

A comprehensive 1000 Genomes–based genome-wide association meta-analysis of coronary artery disease

(2015) Majid Nikpay et al.   NATURE GENETICS

SpeedSeq: ultra-fast personal genome analysis and interpretation

(2015) Colby Chiang et al.   NATURE METHODS

eQTL mapping identifies insertion- and deletion-specific eQTLs in multiple tissues

(2015) Jinyan Huang et al.   Nature Communications

Wham: Identifying Structural Variants of Biological Consequence

(2015) Zev N. Kronenberg et al.   PLoS Computational Biology

Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation

(2015) Momoko Horikoshi et al.   PLoS Genetics

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

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

(2014) Martin Kircher et al.   NATURE GENETICS

Functional annotation of noncoding sequence variants

(2014) Graham R S Ritchie et al.   NATURE METHODS

A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

(2014) Jared O'Connell et al.   PLoS Genetics

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

(2013) S. B. Montgomery et al.   GENOME RESEARCH

Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant

(2013) Rodrigo Almeida et al.   HUMAN MOLECULAR GENETICS

Genome-wide association study identifies three novel loci for type 2 diabetes

(2013) Kazuo Hara et al.   HUMAN MOLECULAR GENETICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

(2013) Ekta Khurana et al.   SCIENCE

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

(2012) Goo Jun et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2012)   NATURE

Rate of de novo mutations and the importance of father’s age to disease risk

(2012) Augustine Kong et al.   NATURE

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   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

A linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

African Genetic Diversity: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping

(2008) Michael C. Campbell et al.   Annual Review of Genomics and Human Genetics