Adding a Variant Annotation Database

Click the + Add variant annotations button under the Variant annotations section header on the library file management page.

If you are using a human - hg19 assembly, variant annotation databases from various sources will appear in the Variant annotation drop-down list (Figure 1). Available variant annotation database sources include:

• dbSNP

• Kaviar

• NHLBI Variant Server

• 1000 Genomes

Multiple versions of the above databases are available. For human - hg38, only dbSNP is currently available. This list is periodically updated.

Figure 1. For human - hg19, automatic downloads of various variant annotation databases are available from the Partek repository

Choose a database from the drop-down list, select the Download variant database radio button and click Create.

If you prefer to add a custom variant annotation database, perhaps from another source or 'gold-standard' validated variants, choose Add variant database from the Variant annotation drop-down list (Figure 2). Name the variant annotation database by typing into the Custom Name box and click Create. Characters such as $ * | \ : " < > ? / % cannot be used in custom names. A variant annotation database can be added from the Partek Flow Server or a URL download link. The behavior of each option is similar to when importing a reference sequence (see Adding a Reference Sequence). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible (.vcf and various compressed formats).

Figure 2. Add a custom variant annotation database

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.