Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

HA Hatherell, C Colijn, HR Stagg, C Jackson… - BMC medicine, 2016 - Springer
Background Whole genome sequencing (WGS) is becoming an important part of
epidemiological investigations of infectious diseases due to greater resolution and cost …

Regulatory variants: from detection to predicting impact

E Rojano, P Seoane, JAG Ranea… - Briefings in …, 2019 - academic.oup.com
Variants within non-coding genomic regions can greatly affect disease. In recent years,
increasing focus has been given to these variants, and how they can alter regulatory …

Scaling accurate genetic variant discovery to tens of thousands of samples

R Poplin, V Ruano-Rubio, MA DePristo, TJ Fennell… - BioRxiv, 2017 - biorxiv.org
Comprehensive disease gene discovery in both common and rare diseases will require the
efficient and accurate detection of all classes of genetic variation across tens to hundreds of …

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

MA Eberle, E Fritzilas, P Krusche, M Källberg… - Genome …, 2017 - genome.cshlp.org
Improvement of variant calling in next-generation sequence data requires a comprehensive,
genome-wide catalog of high-confidence variants called in a set of genomes for use as a …

Systematic comparison of variant calling pipelines using gold standard personal exome variants

S Hwang, E Kim, I Lee, EM Marcotte - Scientific reports, 2015 - nature.com
The success of clinical genomics using next generation sequencing (NGS) requires the
accurate and consistent identification of personal genome variants. Assorted variant calling …

Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencers

J Chen, X Li, H Zhong, Y Meng, H Du - Scientific reports, 2019 - nature.com
The development and innovation of next generation sequencing (NGS) and the subsequent
analysis tools have gain popularity in scientific researches and clinical diagnostic …

The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species

M Lefouili, K Nam - Scientific reports, 2022 - nature.com
Identification of genetic variations is a central part of population and quantitative genomics
studies based on high-throughput sequencing data. Even though popular variant callers …

Genetic variation in the human cytochrome P450 supergene family

K Fujikura, M Ingelman-Sundberg… - Pharmacogenetics and …, 2015 - journals.lww.com
Objectives Single nucleotide variations (SNVs) in the cytochrome P450 (CYP) gene family
are a primary cause of interindividual differences in therapeutic effects and adverse …

Comparison of GATK and DeepVariant by trio sequencing

YL Lin, PC Chang, C Hsu, MZ Hung, YH Chien… - Scientific Reports, 2022 - nature.com
While next-generation sequencing (NGS) has transformed genetic testing, it generates large
quantities of noisy data that require a significant amount of bioinformatics to generate useful …

[HTML][HTML] From next-generation resequencing reads to a high-quality variant data set

SP Pfeifer - Heredity, 2017 - nature.com
Sequencing has revolutionized biology by permitting the analysis of genomic variation at an
unprecedented resolution. High-throughput sequencing is fast and inexpensive, making it …