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