Exporting Sets as Text or VCF Files

To export a set from the Set List and save it as a text (.txt) or Variant Call Format (.vcf) file:

1)  Create and name a set of genes, SNPs, exons, etc.

2)  Open the Set List view by selecting Data > Show Set List.

3)  Select one of the sets. Then, do any of the following:

•      Right-click and choose Export.

•      Select File > Export Selected Set.

•      Click the Export Selected Set tool.

4)  In the Export Names from Set dialog, specify a location, name and file type.

•      If you selected a gene set, the names for each gene in the set will be exported as a .txt file. You can assign the data column to be used as the gene name by modifying Gene Information Settings.

•      If you selected a SNP set, all SNPs in the set will be exported as a Variant Call Format (.vcf) file.

5)  Press the Save button. Unless a multiple-assembly project is open, this concludes the export procedure.

6)  (Multiple-assembly project only). If you are working with a project containing both RNA-Seq and variant data, the Choose experiments dialog will open.

7)  Check or uncheck experiment boxes, as desired. If one or more boxes are checked, ArrayStar will export a sample VCF file for each of the checked items. If no boxes are checked, ArrayStar will export an annotation-only VCF of the type exported in Lasergene version 13.

See VCF File Columns for a description of three columns that make up part of an exported .vcf file.