dbVar houses over 3 million submitted structural variants (SSV) from 120 human studies including copy number variations (CNV), insertions, deletions, inversions, translocations, and complex chromosomal rearrangements. Users can submit multiple SSVs to dbVAR that are presumably identical, but were ascertained by different platforms and samples, to calculate whether the variant is rare or common in the population and allow for cross validation. However, because SSV genomic location reporting can vary - including fuzzy locations where the start and/or end points are not precisely known - analysis, comparison, annotation, and reporting of SSVs across studies can be difficult. This project was initiated by the Structural Variant Comparison Group for the purpose of generating a non-redundant set of genomic regions defined by counts of concordance for all human SSVs placed on RefSeq assembly GRCh38 (RefSeq accession GCF_000001405.26). We intend that the availability of these regions, called structural variant clusters (SVCs), will facilitate the analysis, annotation, and exchange of SV data and allow for simplified display in genomic sequence viewers for improved variant interpretation. Sets of SVCs were generated by variant type for each of the 120 studies as well as for a combined set across all studies. Starting from 3.64 million SSVs, 2.5 million and 3.4 million non-redundant SVCs with count >=1 were generated by variant type for each study and across all studies, respectively. In addition, we have developed utilities for annotating, searching, and filtering SVC data in GVF format for computing summary statistics, exporting data for genomic viewers, and annotating the SVC using external data sources.
Pubmed ID: 28357035 RIS Download
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Structural variation database designed to store data on variant DNA > / = 1 bp in size from all organisms. Associations of defined variants with phenotype information is also provided. Users can browse data containing number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals.
View all literature mentionsA web-based hosting service for software development projects that use the Git revision control system offering powerful collaboration, code review, and code management. It offers both paid plans for private repositories, and free accounts for open source projects. Large or small, every repository comes with the same powerful tools. These tools are open to the community for public projects and secure for private projects. Features include: * Integrated issue tracking * Collaborative code review * Easily manage teams within organizations * Text entry with understated power * A growing list of programming languages and data formats * On the desktop and in your pocket - Android app and mobile web views let you keep track of your projects on the go.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.
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