Convert to VCF file

This guide explains how to convert genotyping reports to VCF files. It provides step-by-step instructions on uploading the necessary files, specifying output file name and species ploidy, running the analysis, and downloading the VCF file.

Alex Sandercock
11 steps
20 seconds

BIGapp works with VCF files. If you do not have a VCF file, but have a DArT Dose file as well as a DArT Counts file, you can use BIGapp to convert those files into a VCF that can be used in the rest of the application. We are continually adding support for new file types.\ \ If you already have a VCF, you can use that, even if it did not come from DArT and can skip this part of the training materials.

On the left hand menu, click "Convert to VCF".

Convert to VCF option highlighted in main BIGapp menu

To upload the DArTag Dosage Report or an AgriSeq report, click on the selection box under the "Select File Format".

Select File format option of DArT Dosage Report highlighted

Next, choose the dose report by clicking on "browse".

Choose DArT Dose Report File "browse" option highlighted

Select the dose report and click "open".

DArT allele dose report highlighted from other file options

Click on "browse" to choose the DArT Counts File. Choose your file and then click open.

Choose DArT counts file browse option highlighted

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

Choose output file name input spot highlighted

Select the species ploidy.

Click "Download VCF File" and retrieve the file from the downloads. You can view the status bar below the "Run Analysis" and "Download VCF File" buttons.

In the informational tab next to the green arrow users can view example input files. These files give examples of the kind of files that are appropriate to upload. This button also provides test data that users can use to test the BIGapp.

Yellow "i" informational button highlighted

An example dose report and counts file are available for users.

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

You can also view a summary of the report creation by clicking on the "summary" box at the bottom.

You have completed this training module. Return to the main BIGapp training page to learn more about the apps various features.