Reports Help

Center for Mendelian Genomics Reports :

  • Data Sharing: Generates the biannual CMG Data Sharing Report. The 1st worksheet is formatted as required by NIH (one phenotype per row). The 2nd worksheet contains the same information, but by sample. The data in the 2nd worksheet can be used to double-check the grouped data in the 1st worksheet, if questions arise.
  • Gene Discovery: This report has not been created.

dbGaP Submission :

NOTE: Data is submitted to dbGaP on a sequencing event. This system defines a sequencing event as a combination of a sample_ID and the date that sequencing data is available for that sample.

  • All Samples / JHU Samples / BCM Samples: Generates a report with dbGaP-related data by sample.
  • Create dbGaP Submission: Accepts and Stores the dbGaP masterfile (which can be created using a tool listed below). Optionally, will parse the uploaded masterfile to populate submission-level on the sequencing events listed in the masterfile.
  • List dbGaP Submission: Lists previously created dbGaP submissions.
  • Upload spreadsheet to create dbGaP Masterfile: Accepts a 2-column file (template available) listing sequencing events. Returns a partially complete dbGaP masterfile.
  • Upload dbGaP information spreadsheet: Provides a mechanism for bulk updates of dbGaP-related information on sequencing events.

So how do I get what I want and need?

  1. How do I know what data is ready to go to dbGaP?
    You have 2 options. Look at the 2nd worksheet of the Data Sharing Report OR run the All samples / JHU Samples / BCM samples query.
  2. How do I know what has already been sent to dbGaP?
    The answer is the same as 1. above. You have 2 options. Look at the 2nd worksheet of the Data Sharing Report OR run the All samples / JHU Samples / BCM samples query.
  3. How do I prepare a masterfile for dbGaP?
    You can get much of the data that you need for the masterfile by utilizing the "Uploading spreadsheet to create dbGaP Masterfile" tool. This requires an input file (which is available for download) that lists the sequencing events (sample_ID and date sequencing data is available) that you want to include in the masterfile.
  4. How do I get dbGaP-related information (dbGaP biosample ID, date data sent to dbGaP, etc) into the database?
    There are 2 mechanisms for doing this. The "Create dbGaP submission" option allows you to store a copy of the masterfile in the database for future reference. It also optionally populates dbGaP information on the sequencing events in the file. This includes dbGaP submission name, date submitted to dbGaP, and date data was available to the public (It does not include biosample ID). Another option is to use the "dbGaP information spreadsheet" to upload this dbGaP-associated information. This mechanism does not store the dbGaP masterfile in the database but does include the biosample id information.