Cargando…

Impact of post-alignment processing in variant discovery from whole exome data

BACKGROUND: GATK Best Practices workflows are widely used in large-scale sequencing projects and recommend post-alignment processing before variant calling. Two key post-processing steps include the computationally intensive local realignment around known INDELs and base quality score recalibration...

Descripción completa

Detalles Bibliográficos
Autores principales:	Tian, Shulan, Yan, Huihuang, Kalmbach, Michael, Slager, Susan L.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2016
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5048557/ https://www.ncbi.nlm.nih.gov/pubmed/27716037 http://dx.doi.org/10.1186/s12859-016-1279-z

Ejemplares similares

Comparative analysis of de novo assemblers for variation discovery in personal genomes
por: Tian, Shulan, et al.
Publicado: (2017)

An analytical workflow for accurate variant discovery in highly divergent regions
por: Tian, Shulan, et al.
Publicado: (2016)

The impact of post-alignment processing procedures on whole-exome sequencing data
por: Borges, Murilo Guimarães, et al.
Publicado: (2020)

Identification of factors associated with duplicate rate in ChIP-seq data
por: Tian, Shulan, et al.
Publicado: (2019)

Whole‐exome sequencing for variant discovery in blepharospasm
por: Tian, Jun, et al.
Publicado: (2018)

JWES: a new pipeline for whole genome/exome sequence data processing, management, and gene‐variant discovery, annotation, prediction, and genotyping
por: Ahmed, Zeeshan, et al.
Publicado: (2021)

Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping
por: Ahmed, Zeeshan, et al.
Publicado: (2021)

Mutation discovery in mice by whole exome sequencing
por: Fairfield, Heather, et al.
Publicado: (2011)

Discovery of Variants Underlying Host Susceptibility to Virus Infection Using Whole-Exome Sequencing
por: Leiva-Torres, Gabriel A., et al.
Publicado: (2017)

Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers
por: Callari, Maurizio, et al.
Publicado: (2017)

Epigenetic alteration contributes to the transcriptional reprogramming in T-cell prolymphocytic leukemia
por: Tian, Shulan, et al.
Publicado: (2021)

Discovery of Potential New Gene Variants and Inflammatory Cytokine Associations with Fibromyalgia Syndrome by Whole Exome Sequencing
por: Feng, Jinong, et al.
Publicado: (2013)

Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank
por: Hofmeister, Robin J., et al.
Publicado: (2023)

An integrative variant analysis suite for whole exome next-generation sequencing data
por: Challis, Danny, et al.
Publicado: (2012)

EXCAVATOR: detecting copy number variants from whole-exome sequencing data
por: Magi, Alberto, et al.
Publicado: (2013)

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

Whole-Exome Sequencing Identifies Damaging de novo Variants in Anencephalic Cases
por: Wang, Linlin, et al.
Publicado: (2019)

Allele-specific copy-number discovery from whole-genome and whole-exome sequencing
por: Wang, WeiBo, et al.
Publicado: (2015)

Experimental Study of Somatic Variants of Osteosarcoma by Whole-Exome Sequencing
por: Hou, Jingyu, et al.
Publicado: (2020)

A domestic cat whole exome sequencing resource for trait discovery
por: Rodney, Alana R., et al.
Publicado: (2021)

PaCBAM: fast and scalable processing of whole exome and targeted sequencing data
por: Valentini, Samuel, et al.
Publicado: (2019)

CANOES: detecting rare copy number variants from whole exome sequencing data
por: Backenroth, Daniel, et al.
Publicado: (2014)

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

A new tool for prioritization of sequence variants from whole exome sequencing data
por: Glanzmann, Brigitte, et al.
Publicado: (2016)

Pathogenic variants identified by whole-exome sequencing in 43 patients with epilepsy
por: Zhang, Linlin, et al.
Publicado: (2020)

Calculating genetic risk for dysfunction in pleiotropic biological processes using whole exome sequencing data
por: Veatch, Olivia J., et al.
Publicado: (2022)

Whole-exome sequencing reveals the impact of UVA light mutagenesis in xeroderma pigmentosum variant human cells
por: Moreno, Natália Cestari, et al.
Publicado: (2020)

Variant detection sensitivity and biases in whole genome and exome sequencing
por: Meynert, Alison M, et al.
Publicado: (2014)

Whole-exome sequencing identifies variants in invasive pituitary adenomas
por: Lan, Xiaolei, et al.
Publicado: (2016)

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

DEVOUR: Deleterious Variants on Uncovered Regions in Whole-Exome Sequencing
por: Türk, Erdem, et al.
Publicado: (2023)

Whole Exome Sequencing Reveals Novel Variants in Unexplained Erythrocytosis
por: Khurana, Harshit, et al.
Publicado: (2023)

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

Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemia
por: Dong, Weilai, et al.
Publicado: (2022)

Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants
por: Kim, Kyung, et al.
Publicado: (2015)

Whole exome capture in solution with 3 Gbp of data
por: Bainbridge, Matthew N, et al.
Publicado: (2010)

Immune monitoring technology primer: whole exome sequencing for neoantigen discovery and precision oncology
por: Kvistborg, Pia, et al.
Publicado: (2016)

Complications of whole-exome sequencing for causal gene discovery in primary platelet secretion defects
por: Gorski, Marcin M., et al.
Publicado: (2019)

Novel pathogenic variants and genes for myopathies identified by whole exome sequencing
por: Hunter, Jesse M, et al.
Publicado: (2015)

Whole-Exome Sequencing Enables the Diagnosis of Variant-Type Xeroderma Pigmentosum
por: Fang, Xiaokai, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_rjp7h2e65nrvcv39m0vivlcsq3