To convert a VCF file to a BED file
1. On the Geneticist Assistant main menu, click Tools > Convert VCF File to BED File.
The Convert VCF to BED dialog box opens.
2. Next to the Source field, click the Browse button 
to open the Open dialog box, and then browse to and select the appropriate VCF file.
to open the Open dialog box, and then browse to and select the appropriate VCF file.3. Indicate how the regions are to created in the BED file.
Option | Description |
|---|---|
Gene | Adds the entire region for the gene in which each variant is found to the BED file. For example, if the variant is found in the BRCA1 gene, then the entire BRCA1 region is added to the BED file. |
Exons Coding | Adds the coding exon for each variant in the VCF file as a region in the BED file. |
Exons All | Adds both the coding exons and the non-coding exons for each variant in the VCF file as a region in the BED file. |
Region | Creates a region for each variant found in the VCF file, based on the variant’s position. If you select Region, then you must also specify the total number of bps that are to be found in each region (the Group by Bases value) with one half of the total number of bps found on each side of the variant position. For example, if you specify 10,000 for Group by Bases, then 5000 bps are found on either side of the variant position for the BED file region. |
4. Click OK.
The Save as dialog box opens.
5. In the Save as dialog box, enter a name and select a location in which to save the BED file, and then click Save.
 | The default name for the BED file is default.BED and the default location in which to save the BED file is the same directory as the source VCF file, but you can change one or both of these values. The file type is .bed and you cannot change this. |
A Convert VCF to BED file message opens, indicating that the conversion is completed.
6. Click OK.
The message closes. The Convert VCF to BED dialog box remains open.
7. Click “x” to close the Convert VCF to BED tool.