12 papers · ranked by Valyu relevance
Weiming He, Lian Xu, JingXian Wang, Zhen Yue + 4 more
'Shuaishuai Tai' 'Jian Yang' 'Xiaodong Fang'] Principal component analysis (PCA) is an important and widely used unsupervised learning method that determines population structure based on genetic variation. Genome sequencing of thousands of individuals usually generate tens of millions of SNPs, making it challenging…
Lian Xu, Weiming He, Shuaishuai Tai, Xiaoli Huang + 7 more
Two tools, VCF2PopTree and fastreeR, offer functions for pairwise distance calculation and for constructing population phylogeny directly from VCF files (Table [tbl1]). However, VCF2PopTree, a JavaScript-based local client program, failed to process datasets with a large number of samples and variants (e.g., 91 samples…
Martin Kapun
patterns in genomic data of Drosophila melanogaster Authors: ['Martin Kapun'] Chromosomal inversions are structural mutations resulting in the reversal of the gene order along the corresponding genomic region. Due to their influence on recombination patterns, they can have a major influence on genetic variation and the…
Erik Garrison, Zev N. Kronenberg, Eric T. Dawson, Brent S. Pedersen + 2 more
Since its introduction in 2011 the variant call format (VCF) has been widely adopted for processing DNA and RNA variants in practically all population studies-as well as in somatic and germline mutation studies. The VCF format can represent single nucleotide variants, multi-nucleotide variants, insertions and…
Tim Dunn, Justin M. Zook, James M. Holt, Satish Narayanasamy
In this work, we extend vcfdist to be the first variant call benchmarking tool to jointly evaluate phased single-nucleotide polymorphisms (SNPs), small insertions/deletions (INDELs), and structural variants (SVs) for the whole genome. First, we find that a joint evaluation of small and structural variants uniformly…
Erik Garrison, Zev N. Kronenberg, Eric T. Dawson, Brent S. Pedersen + 1 more
Since its introduction in 2011 the variant call format (VCF) has been widely adopted for processing DNA and RNA variants in practically all population studies — as well as in somatic and germline mutation studies. VCF can present single nucleotide variants, multi-nucleotide variants, insertions and deletions, and…
Subhayan Chattopadhyay, Jenny Karlsson, Anders Valind, Natalie Andersson + 1 more
Clonal deconvolution of mutational landscapes is crucial to understand the evolutionary dynamics of cancer. Two limiting factors for clonal deconvolution that have remained unresolved are variation in tumor cell fraction (TCF) and chromosomal copy number across different samples of the same tumor. We developed a…
Elizabeth Tseng, Qiandong Zeng, Lax Iyer
We had developed VCFCons to address urgent need for a robust consensus sequence generator for SARS-CoV-2 viral surveillance, which presented several unique requirements, including: (a) low coverage areas should be noted with ‘N’s, (b) low frequency or suspicious variant calls need to be filtered. We have found that…
Tim Dunn, Justin M. Zook, James M. Holt, Satish Narayanasamy
Recent improvements in long-read sequencing accuracy have enabled calling phased small and structural variants from a single analysis pipeline. Despite this, the current standard tools for variant calling evaluation are only designed for either small (vcfeval) or large (Truvari) variants. In this work we extend vcfdist…
Aditya Shastri, Kapil Ahuja, Milind B. Ratnaparkhe, Aditya Shah + 2 more
'Aishwary Gagrani' 'Anant Lal'] Abstract: We develop a Vector Quantized Spectral Clustering (VQSC) algorithm that is a combination of Spectral Clustering (SC) and Vector Quantization (VQ) sampling for grouping Soybean genomes. The inspiration here is to use SC for its accuracy and VQ to make the algorithm…
Brian J. Knaus, Niklaus J. Grünwald
Software to call single nucleotide polymorphisms or related genetic variants has converged on the variant call format (VCF) as the output format of choice. This has created a need for tools to work with VCF files. While an increasing number of software exists to read VCF data, many only extract the genotypes without…
Cristina Moraru, Hany Anany
Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called “megataxonomy of viruses”, recognizes six different viral realms, defined based on the presence of viral hallmark genes (VHGs). Within the realms, viruses are classified into…