xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments

xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments

(2023) Jesse Farek et al.   GigaScience

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

(2022) Marta Byrska-Bishop et al.   CELL

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

(2021) Daniel Taliun et al.   NATURE

HTSlib: C library for reading/writing high-throughput sequencing data

(2021) James K Bonfield et al.   GigaScience

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

A robust benchmark for detection of germline large deletions and insertions

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

Best practices for variant calling in clinical sequencing

(2020) Daniel C. Koboldt   Genome Medicine

A multi-task convolutional deep neural network for variant calling in single molecule sequencing

(2019) Ruibang Luo et al.   Nature Communications

NGSEP3: accurate variant calling across species and sequencing protocols

(2019) Daniel Tello et al.   BIOINFORMATICS

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

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

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

A research roadmap for next-generation sequencing informatics

(2016) Russ B. Altman et al.   Science Translational Medicine

Extensive sequencing of seven human genomes to characterize benchmark reference materials

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

Unified representation of genetic variants

(2015) Adrian Tan et al.   BIOINFORMATICS

A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases

(2015) Neil A. Miller et al.   Genome Medicine

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

(2015) Christopher C Chang et al.   GigaScience

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

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Efficient storage of high throughput DNA sequencing data using reference-based compression

(2011) M. Hsi-Yang Fritz et al.   GENOME RESEARCH

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH