VCF Filtering

This guide provides step-by-step instructions on how to filter VCF data with specific parameters through the BIGapp. By following these steps, users can easily navigate to the website, input their VCF file, set filtering parameters such as ploidy and missing data thresholds, and generate filtered VCF files for download.

Alex Sandercock
16 steps
2 minutes

127.0.0.1

On the left hand menu, click "VCF Filtering".

Left hand menu item "VCF filtering" highlighted

Click "Browse..." and select the VCF file to upload.

Click this button to view example input files. Click this button to 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.

Click the "Output File Name" field and type the desired name for the filtered VCF output.

Click the "Ploidy" field and enter the ploidy of the species.

Click the "MAF filter" field. Users can use the arrows to change the filter level.

MAF filter section with arrows to change selection highlighted

Users can also use the ruler feature to adjust read depth filter.

Click the "Remove SNPs with >= % missing data" field. Enter the missing data percentage for filtering.

Click the "Remove Samples with >= % missing data" field. Enter the missing data percentage for filtering.

Remove samples with missing data section highlighted

If your VCF file was generating using the Updog Dosage Calling tab, then additional VCF filtering parameters are available.\ \ Note: If you use a VCF file that was generated from a different tab or an external tool, the Updog filtering parameters will not be applied.

Optional: Click the "Use Updog Filtering Parameters?" field. If the VCF file was processed through the Updog Dosage Calling tab, then these filtering parameters can be applied.

Use Updog filtering capabilities checkbox highlighted

Click "Apply filters".

Once the filters have been applied, a user can click on the different tabs to the right to view histograms of the filtering statistics.

Click here to adjust the number of the histogram bins.

Histogram bin adjustments section highlighted

View the number of SNPs retained and the percentage of SNPs removed during filtering to the right of where the histograms are located.

SNPs retained and Percent SNPs Removed highlighted

Click this button to view the save image options.

Click here to adjust the figure size and resolution.

Click "Save" to download the selected figure.

Click "Download Filtered VCF" to save the filtered VCF.

Download filtered VCF selection highlighted

You have completed the VCF Filtering module of this training. Please return to the main training menu to learn more about other BIGapp features.