Cargando…

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

BACKGROUND: To facilitate the clinical implementation of genomic medicine by next-generation sequencing, it will be critically important to obtain accurate and consistent variant calls on personal genomes. Multiple software tools for variant calling are available, but it is unclear how comparable th...

Descripción completa

Detalles Bibliográficos
Autores principales:	O'Rawe, Jason, Jiang, Tao, Sun, Guangqing, Wu, Yiyang, Wang, Wei, Hu, Jingchu, Bodily, Paul, Tian, Lifeng, Hakonarson, Hakon, Johnson, W Evan, Wei, Zhi, Wang, Kai, Lyon, Gholson J
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2013
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706896/ https://www.ncbi.nlm.nih.gov/pubmed/23537139 http://dx.doi.org/10.1186/gm432

Ejemplares similares

Genome-wide variant analysis of simplex autism families with an integrative clinical-bioinformatics pipeline
por: Jiménez-Barrón, Laura T., et al.
Publicado: (2015)

Reducing INDEL calling errors in whole genome and exome sequencing data
por: Fang, Han, et al.
Publicado: (2014)

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data
por: Wei, Zhi, et al.
Publicado: (2011)

Accurate detection of de novo and transmitted indels within exome-capture data using micro-assembly
por: Narzisi, Giuseppe, et al.
Publicado: (2014)

Improving bioinformatic pipelines for exome variant calling
por: Ji, Hanlee P
Publicado: (2012)

SeqMule: automated pipeline for analysis of human exome/genome sequencing data
por: Guo, Yunfei, et al.
Publicado: (2015)

Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing
por: Cagirici, H. Busra, et al.
Publicado: (2021)

Systematic comparison of variant calling pipelines using gold standard personal exome variants
por: Hwang, Sohyun, et al.
Publicado: (2015)

Integrating precision medicine in the study and clinical treatment of a severely mentally ill person
por: O’Rawe, Jason A., et al.
Publicado: (2013)

Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data
por: Kumaran, Manojkumar, et al.
Publicado: (2019)

Systematic data-querying of large pediatric biorepository identifies novel Ehlers-Danlos Syndrome variant
por: Desai, Akshatha, et al.
Publicado: (2016)

From Wet‐Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing
por: Laurie, Steve, et al.
Publicado: (2016)

Topographic Mapping as a Basic Principle of Functional Organization for Visual and Prefrontal Functional Connectivity
por: O’Rawe, Jonathan F., et al.
Publicado: (2020)

Topographic organization of the human caudate functional connectivity and age-related changes with resting-state fMRI
por: O'Rawe, Jonathan F., et al.
Publicado: (2022)

NAA10-related syndrome
por: Wu, Yiyang, et al.
Publicado: (2018)

Whole-Exome Sequencing for the Identification of Susceptibility Genes of Kashin–Beck Disease
por: Yang, Zhenxing, et al.
Publicado: (2014)

Improved Variant Calling Accuracy by Merging Replicates in Whole-Exome Sequencing Studies
por: Zhang, Yanfeng, et al.
Publicado: (2014)

Functional neural network configuration in late childhood varies by age and cognitive state
por: Le, Thang M., et al.
Publicado: (2020)

ReliableGenome: annotation of genomic regions with high/low variant calling concordance
por: Popitsch, Niko, et al.
Publicado: (2017)

Precise Identification of Recurrent Somatic Mutations in Oral Cancer Through Whole-Exome Sequencing Using Multiple Mutation Calling Pipelines
por: Lin, Li-Han, et al.
Publicado: (2021)

Validation and assessment of variant calling pipelines for next-generation sequencing
por: Pirooznia, Mehdi, et al.
Publicado: (2014)

ToTem: a tool for variant calling pipeline optimization
por: Tom, Nikola, et al.
Publicado: (2018)

HaploTypo: a variant-calling pipeline for phased genomes
por: Pegueroles, Cinta, et al.
Publicado: (2020)

Association of a rare NOTCH4 coding variant with systemic sclerosis: a family-based whole exome sequencing study
por: Cardinale, Christopher J., et al.
Publicado: (2016)

Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling
por: Zhang, Guoqiang, et al.
Publicado: (2015)

LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data
por: Fang, Li, et al.
Publicado: (2019)

SeqHBase: a big data toolset for family based sequencing data analysis
por: He, Min, et al.
Publicado: (2015)

Accuracy and efficiency of germline variant calling pipelines for human genome data
por: Zhao, Sen, et al.
Publicado: (2020)

A three-caller pipeline for variant analysis of cancer whole-exome sequencing data
por: Liu, Ze-Kun, et al.
Publicado: (2017)

Common variants in polygenic schizophrenia
por: Glessner, Joseph T, et al.
Publicado: (2009)

A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing
por: Andreu-Sánchez, Sergio, et al.
Publicado: (2021)

Whole-genome sequencing in an autism multiplex family
por: Shi, Lingling, et al.
Publicado: (2013)

Protocol for unbiased, consolidated variant calling from whole exome sequencing data
por: Verrou, Kleio-Maria, et al.
Publicado: (2022)

VariantMetaCaller: automated fusion of variant calling pipelines for quantitative, precision-based filtering
por: Gézsi, András, et al.
Publicado: (2015)

appreci8: a pipeline for precise variant calling integrating 8 tools
por: Sandmann, Sarah, et al.
Publicado: (2018)

CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data
por: Packer, Jonathan S., et al.
Publicado: (2016)

Preschool negative emotionality predicts activity and connectivity of the fusiform face area and amygdala in later childhood
por: Kann, Sarah J., et al.
Publicado: (2017)

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
por: Wang, Kai, et al.
Publicado: (2010)

Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement
por: Wang, Kai, et al.
Publicado: (2013)

GPU-accelerated and pipelined methylation calling
por: Feng, Yilin, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_4d95r9h2tas0ldkq511p6ffs8f