Cargando…

VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity

VCF2CNA is a tool (Linux commandline or web-interface) for copy-number alteration (CNA) analysis and tumor purity estimation of paired tumor-normal VCF variant file formats. It operates on whole genome and whole exome datasets. To benchmark its performance, we applied it to 46 adult glioblastoma and...

Descripción completa

Detalles Bibliográficos
Autores principales:	Putnam, Daniel K., Ma, Xiaotu, Rice, Stephen V., Liu, Yu, Newman, Scott, Zhang, Jinghui, Chen, Xiang
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group UK 2019
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6637131/ https://www.ncbi.nlm.nih.gov/pubmed/31316100 http://dx.doi.org/10.1038/s41598-019-45938-x

Ejemplares similares

Sparse Project VCF: efficient encoding of population genotype matrices
por: Lin, Michael F, et al.
Publicado: (2020)

VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files
por: Hart, Steven N., et al.
Publicado: (2016)

genozip: a fast and efficient compression tool for VCF files
por: Lan, Divon, et al.
Publicado: (2020)

GEN2VCF: a converter for human genome imputation output format to VCF format
por: Shin, Dong Mun, et al.
Publicado: (2020)

BrowseVCF: a web-based application and workflow to quickly prioritize disease-causative variants in VCF files
por: Salatino, Silvia, et al.
Publicado: (2017)

A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar
por: Garrison, Erik, et al.
Publicado: (2022)

vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration
por: Dolin, Robert H., et al.
Publicado: (2021)

VIVA (VIsualization of VAriants): A VCF File Visualization Tool
por: Tollefson, G. A., et al.
Publicado: (2019)

VCF2CAPS–A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset
por: Wesołowski, Wojciech, et al.
Publicado: (2021)

VCF-kit: assorted utilities for the variant call format
por: Cook, Daniel E, et al.
Publicado: (2017)

Insane in the vembrane: filtering and transforming VCF/BCF files
por: Hartmann, Till, et al.
Publicado: (2022)

Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files
por: Ebbert, Mark TW, et al.
Publicado: (2014)

Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR
por: Beier, Sebastian, et al.
Publicado: (2022)

re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files
por: Karabayev, Daniyar, et al.
Publicado: (2021)

vcf2gwas: Python API for comprehensive GWAS analysis using GEMMA
por: Vogt, Frank, et al.
Publicado: (2021)

VCF‐Server: A web‐based visualization tool for high‐throughput variant data mining and management
por: Jiang, Jianping, et al.
Publicado: (2019)

Vertebral augmentation treatment of painful osteoporotic compression fractures with the Kiva VCF Treatment System
por: Olivarez, Luis M. Rosales, et al.
Publicado: (2011)

VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data
por: Müller, Heiko, et al.
Publicado: (2017)

VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects
por: Ossio, Raul, et al.
Publicado: (2019)

Restoration in Vertebral Compression Fractures (VCF): Effectiveness Evaluation Based on 3D Technology
por: Noriega González, David C., et al.
Publicado: (2022)

Fastq2vcf: a concise and transparent pipeline for whole-exome sequencing data analyses
por: Gao, Xiaoyi, et al.
Publicado: (2015)

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files
por: Sun, Xiaobo, et al.
Publicado: (2018)

Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection
por: Ha, Jungmin, et al.
Publicado: (2019)

Were VCF patients at higher risk of mortality following the 2009 publication of the vertebroplasty “sham” trials?
por: Ong, K. L., et al.
Publicado: (2017)

vcfView: An Extensible Data Visualization and Quality Assurance Platform for Integrated Somatic Variant Analysis
por: O’Sullivan, Brian, et al.
Publicado: (2020)

The FAM104 proteins VCF1/2 promote the nuclear localization of p97/VCP
por: Körner, Maria, et al.
Publicado: (2023)

Cutevariant: a standalone GUI-based desktop application to explore genetic variations from an annotated VCF file
por: Schutz, Sacha, et al.
Publicado: (2021)

Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis
por: Wang, Gaojianyong, et al.
Publicado: (2020)

Four-copy number alteration (CNA)-related lncRNA prognostic signature for liver cancer
por: Cheng, Zhenyun, et al.
Publicado: (2022)

GrabBlur - a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files
por: Stade, Björn, et al.
Publicado: (2014)

VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs
por: Subramanian, Sankar, et al.
Publicado: (2019)

Holistic Therapeutic Approaches Improve Functional Mobility in Patients With Postoperative Vertebral Compression Fracture (VCF): A Case Report
por: Pakhan, Arjavi A, et al.
Publicado: (2023)

GTX.Digest.VCF: an online NGS data interpretation system based on intelligent gene ranking and large-scale text mining
por: Jiang, Yanhuang, et al.
Publicado: (2019)

LiquidCNA: Tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations
por: Lakatos, Eszter, et al.
Publicado: (2021)

CloneCNA: detecting subclonal somatic copy number alterations in heterogeneous tumor samples from whole-exome sequencing data
por: Yu, Zhenhua, et al.
Publicado: (2016)

Stratification of clear cell renal cell carcinoma (ccRCC) genomes by gene-directed copy number alteration (CNA) analysis
por: Thiesen, H.-J., et al.
Publicado: (2017)

seqCNA: an R package for DNA copy number analysis in cancer using high-throughput sequencing
por: Mosen-Ansorena, David, et al.
Publicado: (2014)

Improved ANAP incorporation and VCF analysis reveal details of P2X7 current facilitation and a limited conformational interplay between ATP binding and the intracellular ballast domain
por: Durner, Anna, et al.
Publicado: (2023)

Impact of CNA on AML prognosis
por: Gonzales, Fanny, et al.
Publicado: (2017)

Interactive analysis of large cancer copy number studies with Copy Number Explorer
por: Newman, Scott
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_fd0msgbjboug8elgvtq31s4rkj