Dosage Calling

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.

Alex Sandercock
15 steps
2 minutes

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.

On the left hand menu, click "dosage calling".

Dosage calling option highlighted on the left hand main BIGapp menu

Upload MADC file or VCF file by clicking on "Browse..."

Browse highlighted under "Choose MADC or VCF file" input

Choose your file and click "open".

MADC file highlighted amongst file options

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

Click on "browse" to choose the trait file.

Choose your file and click "open".

Passport file option highlighted amongst other file options

Select a category subset.

Species option underneath the select category subset other options include sample ID, sepal lenght and other options

Select subset values. You may choose more than one.

Versicolor option highlighted under select subset variable

Click the "Output File Name" field and type the desired output file name.

Output file name input section highlighted

Select the species ploidy.

Species ploidy input section highlighted

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.*

Updog model options shown with "norm" choosen and f1 highlighted as another option

Some models will require additional information.

Enter parental ID input section highlighted

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

Number of CPU cores selection input section highlighted

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

Options under informational tab including example files, parameters, results, citation and summary

When you are satisfied with your selections, click "run analysis".

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

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

Dosage Calling

Alex Sandercock
15 steps
2 minutes

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.

On the left hand menu, click "dosage calling".

Upload MADC file or VCF file by clicking on "Browse..."

Choose your file and click "open".

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

Click on "browse" to choose the trait file.

Choose your file and click "open".

Select a category subset.

Select subset values. You may choose more than one.

Click the "Output File Name" field and type the desired output file name.

Select the species ploidy.

Some models will require additional information.

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

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

When you are satisfied with your selections, click "run analysis".

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

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