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

An open resource for accurately benchmarking small variant and reference calls

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

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines

(2018) Somak Roy et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

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

Extensive sequencing of seven human genomes to characterize benchmark reference materials

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

College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests

(2015) Nazneen Aziz et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Unified representation of genetic variants

(2015) Adrian Tan et al.   BIOINFORMATICS

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

(2015) Adam D Ewing et al.   NATURE METHODS

An analytical framework for optimizing variant discovery from personal genomes

(2015) Gareth Highnam et al.   Nature Communications

SM a SH: a benchmarking toolkit for human genome variant calling

(2014) Ameet Talwalkar et al.   BIOINFORMATICS

Solving the molecular diagnostic testing conundrum for Mendelian disorders in the era of next-generation sequencing: single-gene, gene panel, or exome/genome sequencing

(2014) Yuan Xue et al.   GENETICS IN MEDICINE

Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

(2014) Yaping Yang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

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

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

ACMG clinical laboratory standards for next-generation sequencing

(2013) Heidi L. Rehm et al.   GENETICS IN MEDICINE

Assuring the quality of next-generation sequencing in clinical laboratory practice

(2012) Amy S Gargis et al.   NATURE BIOTECHNOLOGY

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A standardized framework for the validation and verification of clinical molecular genetic tests

(2010) Christopher J Mattocks et al.   EUROPEAN JOURNAL OF HUMAN GENETICS