Dosage Calling

Made by Alex Sandercock with Scribe

This guide offers a step-by-step process for performing dosage calling, a crucial task for analyzing genetic data efficiently. By following this guide, users can streamline their workflow and ensure accurate results in their genetic analyses.

Alert: Depending on the dataset size, this could take several hours to complete. An example dataset that has 650 samples and 6,000 markers will take 1-3 hours to complete with 10 cores.

1. On the left hand menu, click “dosage calling”.

2. Upload MADC file or VCF file by clicking on “Browse…”

3. Choose your file and click “open”.

Alert: The following steps are optional to subset the samples in the input file for dosage calling - (Steps 4 - 7)

4. Click on “browse” to choose the trait file.

5. Choose your file and click “open”.

6. Select a category subset.

7. Select subset values. You may choose more than one.

8. Click the “Output File Name” field and type the desired output file name.

9. Select the species ploidy.

10. Click here to select Updog model. The different models are selected depending on how the breeding populations were created.

Please note that “norm” is a catchall model that works well for most situations. To make the best decision for a user’s specific population, refer to the “Help” section within BIGapp.

11. Some models will require additional information.

12. Also select the “Number of CPU Cores” field and choose the number of compute cores you would like to use.

13. An informational box is also available here with summary information and example files.

14. When you are satisfied with your selections, click “run analysis”.

15. Upon completion, a new button will appear. Click “download VCF file” to retrieve a VCF file with the dosage call information.

Tip: You have completed learning about dosage calling through the BIGapp. Return to the main training menu to learn more about other features.