Curated variation benchmarks for challenging medically relevant autosomal genes

Author Correction: A structural variation reference for medical and population genetics

(2021) Ryan L. Collins et al.   NATURE

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression

(2021) Paras Garg et al.   AMERICAN JOURNAL OF HUMAN GENETICS

One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation

(2021) Stephen E. Lincoln et al.   GENETICS IN MEDICINE

Exome variant discrepancies due to reference-genome differences

(2021) He Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Towards population-scale long-read sequencing

(2021) Wouter De Coster et al.   NATURE REVIEWS GENETICS

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

(2021) Kishwar Shafin et al.   NATURE METHODS

Structural Variants May Be a Source of Missing Heritability in sALS

(2020) Frances Theunissen et al.   Frontiers in Neuroscience

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

A robust benchmark for detection of germline large deletions and insertions

(2020) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

(2020) Sergey Nurk et al.   GENOME RESEARCH

A diploid assembly-based benchmark for variants in the major histocompatibility complex

(2020) Chen-Shan Chin et al.   Nature Communications

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

Deep convolutional neural networks for accurate somatic mutation detection

(2019) Sayed Mohammad Ebrahim Sahraeian et al.   Nature Communications

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

(2019) Peter Krusche et al.   NATURE BIOTECHNOLOGY

Similarities and differences between variants called with human reference genome HG19 or HG38

(2019) Bohu Pan et al.   BMC BIOINFORMATICS

An open resource for accurately benchmarking small variant and reference calls

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

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing

(2019) Peter Edge et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

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

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

Rescue of recurrent deep intronic mutation underlying cell type–dependent quantitative NEMO deficiency

(2018) Bertrand Boisson et al.   JOURNAL OF CLINICAL INVESTIGATION

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

(2017) Daniel L. Cameron et al.   GENOME RESEARCH

Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis

(2017) Yan Guo et al.   GENOMICS

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

Navigating highly homologous genes in a molecular diagnostic setting: a resource for clinical next-generation sequencing

(2016) Diana Mandelker et al.   GENETICS IN MEDICINE

Structure, function, and genetics of lipoprotein (a)

(2016) Konrad Schmidt et al.   JOURNAL OF LIPID RESEARCH

Medical implications of technical accuracy in genome sequencing

(2016) Rachel L. Goldfeder et al.   Genome Medicine

Extensive sequencing of seven human genomes to characterize benchmark reference materials

(2016) Justin M. Zook et al.   Scientific Data

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

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

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads

(2015) Murray Patterson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Wham: Identifying Structural Variants of Biological Consequence

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

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

A public resource facilitating clinical use of genomes

(2012) Madeleine P. Ball et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Addition of H19 ‘Loss of Methylation Testing’ for Beckwith-Wiedemann Syndrome (BWS) Increases the Diagnostic Yield

(2010) Jochen K. Lennerz et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS