We have just launched GaPTools, a stand-alone data validation tool for NCBI’s database of Genotype and Phenotype (dbGaP) submissions. You can use GaPTools to validate your dbGaP submissions or submissions to other genomic data repositories. GaPTools checks for common data inconsistency and integrity issues and validates subject-sample ID mapping, subject consents, data dictionaries, and phenotype and genotype data. GaPTools is available as a docker image on Docker Hub.
Why Use GaPTools?
GaPTools will validate files before you submit (see Figure 1). This means that by the time you formally submit, some of the pre-validation steps are already addressed. This tool allows you to prepare your data quickly and ensures a faster processing cycle and a faster release of your individual-level research data.Figure 1: Flow chart depicting data submission and GaPTools validation
dbGaP has recently released a new feature to simplify submissions and provide study accessions faster. This video provides a quick overview of the new feature.
Our new study config webform enables a study submitter to enter important study summary information including study description, inclusion/exclusion criteria, history, attribution, and associated publications online and instantly preview the study config content and study accession on their dbGaP study report page. Study design and type, PMIDs, Genes, MeSH terms, and associated Clinical Trials have built-in help and validation to ensure that the information provided is complete and searchable by users looking for that data.
The database of Genotypes and Phenotypes (dbGaP) provides controlled-access to the data and results from studies that have investigated the interaction of genotype and phenotype in humans. dbGaP assigns stable, unique identifiers to studies and subsets of information from those studies, including documents, individual phenotypic variables, tables of trait data, sets of genotype data, computed phenotype-genotype associations, and groups of study subjects who have given similar consents for use of their data.
The submissions made to dbGaP represent the best and latest research in topic areas such as cardiovascular diseases, diabetes, autism spectrum disorders, precision medicine and many more. Submitters are central to the success of dbGaP and sharing of genomic research across the broader scientific community. Our submission portal serves as a central place to collect multiple components of a research study, including the metadata/summary and associated phenotype, genotype, and sequence data.
Two up-and-coming NCBI resources will be featured in videos, surveys and live events at the American Society for Human Genetics (ASHG) 2020 Annual Meeting. Come and watch on-demand videos in the CoLab Theater. Then, let us know what you think and how you do or might use these resources by either taking an online survey or joining us for the CoLab Live! Events on Thursday, October 29, 2020.
The National Library of Medicine (NLM) is pleased to announce that all controlled-access and publicly available data in SRA is now available through Google Cloud Platform (GCP) and Amazon Web Services (AWS). To access the data please visit our SRA in the Cloud webpage where you will find links to our new SRA Toolkit and other access methods.
The SRA data available in the two clouds currently totals more than 14 petabytes and consists of all data in the SRA format as well as some data in its original submission format. Since May 2019, NCBI has been putting all submitted SRA data on the GCP and AWS clouds in both the submitted format and our converted SRA format. We have also been moving previously submitted original format data to the clouds and expect to complete that process in 2021. Continue reading “The entire corpus of the Sequence Read Archive (SRA) now live on two cloud platforms!”→
Check out the latest videos on YouTube to learn how to best use NCBI graphical viewers, SRA, PGAP, and other resources.
Genome Data Viewer: Analyzing Remote BAM Alignment Files and Other Tips
This video shows you how to upload remote BAM files, and succinctly demonstrates handy viewer settings, such as Pileup display options, and highlights the very helpful tooltips in the Genome Data Viewer (GDV). There’s also a brief blog post on the same topic.
NCBI’s Genetic Relationship and Fingerprinting (GRAF) tool is a quality assurance tool that can quickly find duplicates and closely related subjects in your data using SNP genotypes.
The population tool GRAF-pop included in GRAF computes subject ancestries using genotypes and normalizes ancestry prediction in large datasets collected across different genotyping platforms, making it possible to generate population frequency based on more than a million dbGaP samples.
Who can use this?
GRAF is a tool for researchers; it is not designed to assess an individual’s ancestry or to find relatives.
You can use this tool against your own large datasets with results generated within hours or minutes, even when there is a very high genotype missing rate to the order of 99%. This tool can check genotype datasets obtained using different chips or platforms, plotting them in the same picture for comparison purposes.
Do you need access to controlled data in the database of Genotypes and Phenotypes (dbGaP)? This short video will show you how to request data today!
dbGaP archives and distributes the data and results from studies that have investigated the interaction of genotype and phenotype in humans. Responsible stewardship of controlled-access data subject to the NIH GDS Policy is shared among the NIH, the investigators approved to access the data, and the investigators’ institutions.
Next Wednesday, June 27, 2018, we’ll introduce you to the Genetic Relationship and Fingerprinting (GRAF) software package. GRAF is a quality assurance tool that finds duplicates and closely related subjects in your data using SNP genotypes. We’ll also introduce the GRAF-pop feature, which computes subject ancestries and plots data for export as a .png or .txt file.
Date and time: Wed, June 27 12:00 PM – 12:30 PM EDT
After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.