Step 2. Prepare and Import a Pedigree Spreadsheet

After creating a LogR DSF file, the next step is preparing a pedigree spreadsheet and importing it into your project file.

Golden Helix PBAT supports reading either standard FBAT Pedigree files or Text Pedigree files, which can be space, comma, or tab delimited.

If you have a standard FBAT Pedigree file you will not have to do any further processing except to make sure there is a column (typically the Patient ID column) containing unique names for each sample matching the Sample names in the LogR DSF file (Step 1).

NOTE: If your FBAT Pedigree file contains genotype information, this information will be ignored during CNV analysis.

A Text Pedigree file is recommended because is more robust in that you can exclude ancillary genotype information and easily create a row label column to match the CEL file names in the LogR DSF file. The following is the 30_common_ped.csv file contained in the ZIP file above as viewed in Excel.

Similar to FBAT Pedigree files, this comma-delimited file contains Family ID, Patient ID, Father ID, Mother ID, Sex, and Affection Status. Additionally, it contains column headers as well as a Sample ID column, which will be used as a row label column matching the DSF row label column when performing PBAT CNV analysis.

After you’ve created an FBAT or Text Pedigree file, you need to import it into your project file. To do this, from the main Project Navigator window, go to >PBAT >Import FBAT Pedigree or >PBAT >Import Text Pedigree.

For the purpose of this tutorial open the 30_common_ped.csv file by selecting >PBAT >Import Text Pedigree. The following dialog will open:

From this window Choose the 30_common_ped.csv file and select File format: Comma delimited since it is a CSV file. Then input a 1 in the Row Label Column Number box. This indicates that the first column in the Text Pedigree is to be the row label column.

Click OK. The following dialog will appear informing you how many samples (30 in this case) were imported and which variable types were included.

Click OK. The pedigree spreadsheet in Figure 3 will now be loaded into the project.

Notice the Sample ID column is grayed out, indicating it is the row label column. Also notice that in the top left corner of the spreadsheet, next to Sheet 1, there is a small symbol with a ‘P’ in the middle. This indicates this particular spreadsheet is a pedigree spreadsheet. If your spreadsheet does not have this symbol then something likely went wrong during the import process and PBAT will not recognize it for further copy number analysis.