Results 41 to 50 of about 709,139 (287)

Challenges imposed by minor reference alleles on the identification and reporting of clinical variants from exome data

BMC Genomics, 2018
Background The conventional variant calling of pathogenic alleles in exome and genome sequencing requires the presence of the non-pathogenic alleles as genome references.
Mahmoud Koko, Mohammed O. E. Abdallah, Mutaz Amin, Muntaser Ibrahim   +3 more
doaj   +1 more source

Accurate somatic variant detection using weakly supervised deep learning

Nature Communications, 2022
Deep learning could be applied to the challenge of somatic variant calling in cancer by making use of large-scale genomic data. Here, the authors develop VarNet, a weakly supervised deep learning model for somatic variant calling in cancer with robust ...
Kiran Krishnamachari, Dylan Lu, Alexander Swift-Scott, Anuar Yeraliyev, Kayla Lee, Weitai Huang, Sim Ngak Leng, Anders Jacobsen Skanderup   +7 more
doaj   +1 more source

Psi-Caller: A Lightweight Short Read-Based Variant Caller With High Speed and Accuracy

Frontiers in Cell and Developmental Biology, 2021
With the rapid development of short-read sequencing technologies, many population-scale resequencing studies have been carried out to study the associations between human genome variants and various phenotypes in recent years.
Yadong Liu, Tao Jiang, Yan Gao, Bo Liu, Tianyi Zang, Yadong Wang   +5 more
doaj   +1 more source

Variant Calling Files

, 2022
Variant calling files for the HiC N. nebulosa assembly, the Ragout N. diardi chromosome assembly, and the original scaffold N.
Madeline Bursell (11098476), Rebecca Dikow (7205195)   +1 more
core   +1 more source

Parliament2: Accurate structural variant calling at scale [PDF]

GigaScience, 2020
Abstract Background Structural variants (SVs) are critical contributors to genetic diversity and genomic disease. To predict the phenotypic impact of SVs, there is a need for better estimates of both the occurrence and frequency of SVs, preferably from large, ethnically diverse cohorts.
Samantha Zarate, Andrew Carroll, Medhat Mahmoud, Olga Krasheninina, Goo Jun, William J Salerno, Michael C Schatz, Eric Boerwinkle, Richard A Gibbs, Fritz J Sedlazeck   +9 more
openaire   +2 more sources

BBCAnalyzer: a visual approach to facilitate variant calling [PDF]

BMC Bioinformatics, 2017
Deriving valid variant calling results from raw next-generation sequencing data is a particularly challenging task, especially with respect to clinical diagnostics and personalized medicine. However, when using classic variant calling software, the user usually obtains nothing more than a list of variants that pass the corresponding caller's internal ...
Sarah Sandmann, Aniek O. de Graaf, Martin Dugas   +2 more
openaire   +5 more sources

Are reads required? High-precision variant calling from bacterial genome assemblies [PDF]

Access Microbiology
Ian Monk, Ryan R Wick, Timothy Stinear
exaly   +2 more sources

ADS-HCSpark: A scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark

BMC Bioinformatics, 2019
Background The advance of next generation sequencing enables higher throughput with lower price, and as the basic of high-throughput sequencing data analysis, variant calling is widely used in disease research, clinical treatment and medicine research ...
Anghong Xiao, Zongze Wu, Shoubin Dong
doaj   +1 more source

Estimating sequencing error rates using families

BioData Mining, 2021
Background As next-generation sequencing technologies make their way into the clinic, knowledge of their error rates is essential if they are to be used to guide patient care.
Kelley Paskov, Jae-Yoon Jung, Brianna Chrisman, Nate T. Stockham, Peter Washington, Maya Varma, Min Woo Sun, Dennis P. Wall   +7 more
doaj   +1 more source

Prioritisation of structural variant calls in cancer genomes

PeerJ, 2016
Sensitivity of short read DNA-sequencing for gene fusion detection is improving, but is hampered by the significant amount of noise composed of uninteresting or false positive hits in the data. In this paper we describe a tiered prioritisation approach to extract high impact gene fusion events from existing structural variant calls. Using cell line and
Ahdesmäki, Miika J., Cingolani, Pablo, Hofmann, Oliver, Sidoruk, Aleksandr, Lai, Zhongwu, Zakharov, Gennadii, Rodichenko, Mikhail, Alperovich, Mikhail, Jenkins, David, Carr, T. Hedley, Stetson, Daniel, Dougherty, Brian, Barrett, J. Carl, Johnson, Justin H., Chapman, Brad   +14 more
openaire   +6 more sources