Finding Key Files of Interest in the GREGoR Dataset

The GREGoR Dataset includes a wide range of data and file formats as described in the GREGoR Data Model. Analysts working with GREGoR Data can find file paths to molecular data files using the structure of the Data Model and search features within an AnVIL workspace to find specific information in workspace data tables. We have also compiled the following information about how to find certain files of broad interest.

Locations of key files

Refer to the table below for the information needed to find key files of interest in an AnVIL workspace (step numbers are annotated in the screenshot and specified in the table below).

  1. Log in to AnVIL at anvil.terra.bio.
  2. Navigate to a workspace of interest (recommended to choose the latest shared GREGoR workspace, e.g. AnVIL_GREGoR_R02_GRU).
  3. Navigate to the “DATA” tab from the menu bar at the top.
  4. Search for the text string - as specified in the table below - by entering into the search box under the “TABLES” section in the left sidebar to search across all data tables in the workspace.
  5. Filter your results by selecting the data table - as specified in the table below - from the left sidebar (which you may need to expand).
  6. Refer to the column - as specified in the table below (Step 6a) - and identify rows with the matching text string (Step 6b). You might need to expand the columns in the data table individually to find the specific column of interest. Rows that contain the matching text string in the specified column include paths to the key files of interest.
  7. Select the checkboxes for all the files that match the search criteria to open or export.
     

Screenshot of AnVIL Data Tab harmonized CRAMs

The example above is a screenshot of the results that you may see by searching for harmonized CRAMs following the steps outlined in row 1 of the table below.

For resources on interacting with and analyzing GREGoR data, refer to the AnVIL Resources webpage.
 

Key file(s) Description of the file(s) Step 4: Text string to input into search box Step 5: Data table name containing path(s) to file(s) Step 6a: Column name containing matching text string Step 6b: Text string to ID the right search results
Harmonized CRAMs Alignment files reprocessed by the GREGoR DCC GREGoR_DCC_A1 aligned_dna_short_read aligned_dna_short_read_id “GREGoR_DCC_A1…”
Text string is a prefix.
GVCFs Curated data for release to the general scientific community via dbGaP GREGoR_DCC_A1 called_variants_dna_short_read aligned_dna_short_read_id “GREGoR_DCC_A1…”
Text string is a prefix.