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113 results for “VCF”
VCF file of an individual with a variant in the RLIM gene
<p>The VCF file was obtained from whole-exome sequencing data of a DNA sample from an individual with a likely pathogenic variant in the RLIM gene (MIM 300379), which causes Tønne-Kalscheuer syndrome (MIM 300978).</p> <ul> <li>proband.vcf is a file of an affected individual (proband) with a variant in the RLIM gene.</li> </ul>
Malus species SNP calls VCF
<p>Bgzipped vcf and tabix index files of Malus species SNP calls of 168 individuals on the GDDH13 v1.1 assembly.</p>
JG-based sample vcf file
<p>This file is a vcf file based on JG that has been processed using Chinese Trio fastq after undergoing VQSR. We published this data in an article introducing the utilization of SnpEff.</p>
Annotated VCF of 192 Verticillium dahliae isolates
<p><span></span></p> <p><em>Verticillium dahliae</em> is an important soil-borne pathogen causing Verticillium wilt. It is also the primary causal agent of the Potato Early Dying, a disease complex involving the root-lesion nematode. Here, we report the whole-genome sequencing of 192 isolates of <em>V. dahliae</em> originating from the major potato production areas across Canada. Our results yielded a resource of <span> 277,010 genetic variations</span> that will be useful for genetic analyses and revealed the presence of two major lineages, both present in all provinces but exhibiting differences in regional prevalence.</p>
Joseph Lalli CHM13-T2T Pangenie reference vcf - unofficial
<p>hprc-jun1-mc-chm13.pangenie_panel.bcf.gz: Draft pangenome (Jun1-mc version) in CHM13-T2T coordinates</p> <p>hprc-jun1-mc-chm13.fasta: CHM13 reference paths from Jun1-mc draft pangenome.</p> <p>hprc-jun1-mc-chm13.fasta.fai: Reference index.</p> <p>pangenie.def and pangenie.sif: Singularity container to run Pangenie 2.1</p> <p>run_pangenie.sh: Bash script to run pangenie on HTCondor servers. Specifically, the script downloads a specified 1KGP unaligned cram file, extracts the reads locally, creates a checkpoint .jf kmer count table, and then runs Pangenie on the .jf file. The resulting vcf file is compressed to a bcf.gz file, and is saved in the staging directory.</p> <p>HG02030.pangenie.bcf.gz: An example of the output from the 1KGP sample HG02030.</p>
Chromosome VCF files and 1Mb recombination rate estimations for: Fine-scale recombination rate variation and association with genomic features in a butterfly
<p>Genetic recombination is a key molecular mechanism that has profound implications on both micro- and macro-evolutionary processes. However, the determinants of recombination rate variation in holocentric organisms are poorly understood, in particular in Lepidoptera (moths and butterflies). The wood white butterfly (<em>Leptidea</em> <em>sinapis</em>) shows considerable intraspecific variation in chromosome numbers and is a suitable system for studying regional recombination rate variation and its potential molecular underpinnings. Here, we developed a large whole-genome resequencing data set from a population of wood whites to obtain high-resolution recombination maps using linkage disequilibrium information. The analyses revealed that larger chromosomes had a bimodal recombination landscape, potentially due to interference between simultaneous chiasmata. The recombination rate was significantly lower in subtelomeric regions, with exceptions associated with segregating chromosome rearrangements, showing that fissions and fusions can have considerable effects on the recombination landscape. There was no association between the inferred recombination rate and base composition, supporting a negligible influence of GC-biased gene conversion in butterflies. We found significant but variable associations between the recombination rate and the density of different classes of transposable elements (TEs), most notably a significant enrichment of SINEs in genomic regions with higher recombination rate. Finally, the analyses unveiled significant enrichment of genes involved in farnesyltranstransferase activity in recombination cold-spots, potentially indicating that expression of transferases can inhibit formation of chiasmata during meiotic division. Our results provide novel information about recombination rate variation in holocentric organisms and has particular implications for forthcoming research in population genetics, molecular/genome evolution and speciation.</p>
COVID-19 PBMC sample information and the VCF file of variants around OAS1 gene.
<p>We investigated our recently published PBMC scRNA-seq data (Stephenson et al. 2021 Nat Med) obtained from 112 donors, including 84 COVID-19 positive individuals, and profiled using the CITE-seq approach, as an independent in vivo validation of OAS1 eQTL colocalisation with GWAS locus for COVID-19 susceptibility. The dataset includes both sample information and genotype information of variants around OAS1 gene (chr12:111906777-113906777) as in VCF format. The whole variant data of the COVID-19 PBMC samples is available upon request.</p>
Sniffles2 supporting matetial: VCF
<p>VCF showing the structural variants called by Sniffles and other methods (cuteSV, sniffles1, pbsv, svim, manta, OGM) that are used in the manuscript.<br> Samples included are:</p> <ul> <li>GIAB v0.6 and CMRG (HG002)</li> <li>HG002, HG003, HG004 and trio merge</li> <li>MSA-ONT germline, MSA-ONT mosaic, MSA-ILLUMINA, MSA-OGM (Bionano)</li> <li>COLO829 germline (ONT, Revio), COLO829 mosaic (ONT, Revio), COLO289BL germline (ONT, Revio), COLO289-merge germline, COLO289-merge mosaic</li> </ul>
Unfiltered VCF for pink salmon rapid adaptation
<div> <p>Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (<em>Oncorhynchus gorbuscha</em>) that were accidentally introduced to the Great Lakes via a single introduction event 31-generations ago. Using whole-genome resequencing for 134 fish spanning five sample groups across the native and introduced range, we estimate that the source population's effective population size was 146,886 at the time of introduction, whereas the founding population's effective population size was just 72—a 2040-fold decrease. As expected with a severe founder event, we show reductions in genome-wide measures of genetic diversity, specifically a 37.7% reduction in the number of SNPs and an 8.2% reduction in observed heterozygosity. Despite this decline in genetic diversity, we provide evidence for putative selection at 47 loci across multiple chromosomes in the introduced populations, including missense variants in genes associated with circadian rhythm, immunological response, and maturation, which match expected or known phenotypic changes in the Great Lakes. For one of these genes, we use a species-specific agent-based model to rule out genetic drift and conclude our results support a strong response to selection that occurred in a period gene (per2) that plays a predominant role in determining an organism's daily clock, matching large day-length differences experienced by introduced salmon during important phenological periods. Together, these results inform how populations might evolve rapidly to new environments, even with a small pool of standing genetic variation.</p> </div>
Genotype likelihood (beagle file) and genotype (vcf) files of North Atlantic and Black Sea Harbour porpoises (Phocoena phocoena)
<p><span>The Harbour porpoise (<em>Phocoena phocoena</em>) is a highly mobile cetacean species primarily occurring in coastal and shelf waters across the Northern hemisphere. It inhabits heterogeneous seascapes broadly varying in salinity and temperature. Here we produced 74 whole genomes at intermediate coverage to study Harbour porpoise's evolutionary history and investigate the role of local adaptation in the diversification into subspecies and populations. We identified ~6 million high-quality SNPs sampled at 8 localities across the North Atlantic </span><span>and adjacent waters</span><span>, which we used for population structure, demographic, and genotype-environment association analyses. Our results suggest a genetic differentiation between three subspecies (<em>P.p. relicta</em>, <em>P.p. phocoena,</em> and the recently proposed <em>P.p meridionalis</em>), and three distinct populations within the subspecies <em>P.p. phocoena</em>: Atlantic, Belt Sea, and Proper Baltic Sea. Effective population size and Tajima's D levels suggest a population contraction in Black Sea and Iberian porpoises, but a population expansion in the <em>P.p. phocoena</em> populations</span><span>. </span><span>Phylogenetic trees</span> <span>indicate a post-glacial colonization from a southern refugium. </span><span>Genotype-environment association analysis identified salinity as a major driver in genomic variation and we identified candidate genes putatively underlying adaptation to different salinity levels. </span><span>Our study highlights the value of whole genome resequencing to unravel subtle population structure in highly mobile species, shows how strong environmental gradients and local adaptation may lead to population differentiation and how neutral and adaptive markers give different perspectives on population subdivision. </span><span>The results have great conservation implications as we found inbreeding and low genetic diversity in the endangered Black Sea subspecies and identified the critically endangered Proper Baltic Sea porpoises as a separate population.</span></p>
Unfiltered VCF for pink salmon rapid adaptation
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De novo assembly of SNPs in VCF format for 112 individualss of Campylorhynchus in western Ecuador
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Big cat vcf files from: Exceedingly low genetic diversity in snow leopards due to persistently small population size
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Genotype likelihood (beagle file) and genotype (vcf) files of North Atlantic and Black Sea Harbour porpoises (Phocoena phocoena)
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VCF for neutral data set and potential connectivity matrices of Harpagifer antarcticus, along the Western Antarctic Peninsula
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VCF datasets and analysis scripts for: The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability
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VCF-file for: The effects of GC-biased gene conversion on patterns of genetic diversity among and across butterfly genomes
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Annotated VCF of 192 Verticillium dahliae isolates
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VCF files and regression analyses for: Assessing fine-scale pondscape connectivity with amphibian eyes: an integrative approach using genomic and capture-mark-recapture data
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<em>Scutellaria floridana</em> ddRAD-Seq vcf files
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.