General dbGaP Information

It has become more and more common that cohort samples sequenced within the group must be transferred to dbGaP. It is also becoming essential to download samples from studies hosted on dbGaP to incorporate into local analyses. This guide provides general information on how to manage the data involved in these transfers

dbGaP uploads

It has been the responsibility of the Bioinformatics team to prepare BAM and VCF files for transfer to dbGaP. The IT team has managed the physical data transfer, but they must first be provided a list of paths to the properly formatted data.

dbGaP downloads

Retrieving data from dbGaP involves a lengthy application process for each individual study. Although there may be a need to provide language to the application itself, typically the formal applications have been managed external to the bioinformatics team, most often by a Project Manager or a Clinical Research Coordinator.

Once approval has been granted though, it has been the responsibility within Bioinformatics to assess the available data, automate the transfer of the data, format it appropriately for inclusion into the analysis framework (ATAV/AnnoDB) and communicate the availability of the data to the analyst groups.