User Guide

How it works

VARPIN is variant prioritization software using a ranking methodology based on ANNOVAR returned data. It capable of processing large datasets and also provides additional information for the variant that matched with ACMG recommendation data.

Express Method

This method required minimal data to be submitted. Suitable for a user who already has a setting file or wishes to calculate the input file with the default setting.

On the main webpage of the website. Specify the following data to VARPIN:

The following data is mandatory.

• Input VCF File : Select VCF file that contains variant informations
• Record Name : Name of the record

The following data is optional.

• Setting File : A file that contains a custom variable value. This file can be generated from the setting generator or download from the submitted record. In case the user did not specify a setting file, the system will use the default setting to calculate the submitted file.
• Email-Address : Email Address for receiving notification and new access key of the record. In case no Email Address has been specified, the user will have to save the Access Key of the record manually and the record will unable to reset the Access Key.

Then click "UPLOAD" button to submit the record.

Advance Method

This method provides more control over the calculation setting of the submitted record for the user.

1. Click the "Advanced Setting" button on the main webpage of the website.

The user will be presented with an advanced setting page in which the database, the group can be selected to use in the calculation and variable value can be assigned.



2. On the first page is the General Information Page. Specify the following data to VARPIN:

   The following data is mandatory.
   • Input VCF File : Select VCF file that contains variant informations
   • Record Name : Name of the record
   The following data is optional.
   • Email-Address : Email Address for receiving notification and new access key of the record. In case no Email Address has been specified, the user will have to save the Access Key of the record manually and the record will unable to reset the Access Key.

   Then click "Next >" button to go to Database Selection page.



3. The Second page is Database Selection Page. Users can select a database that users wish to use in the variant calculation process.

   After the selection, click "Next >" Button to go to Display Only Selection page.



4. The third page is the Display Only Selection Page. Users will be able to choose a database from the previous page that will not affect the scoring and filtering process but will display information from the database in the report file.

   After the selection, click "Next >" Button to go to Variable page.



5. The last page is Variable Page. where the value of the variable that will be used in the calculation can be specified.

   • Skip this part : When clicking this button, users will be sent to the upload button positioned at the bottom of the page.
   • Use default value : When the checkbox is checked, the system will use the default value of the current variable in the calculation.

   After database selection, click the "upload" button to submit the record.

After Submit

After the record has been submitted. The user can access the record by using Access Key obtained from the history page or Email Address that the user has provided.

1. In case the record is still in the processing queue, the user will be redirected to the record status page.
2. In case the record has finished processing, the user will be redirected to the report page.

Record Status

This page will be shown if the user accesses the record when it is still processing. Display the current status of the record.

Report Page

This page will be shown if the user accesses the record when the calculation has been done. Display choices of report downloading or record management. The record will be automatically deleted after the expiration time of the record.

• Download : Use buttons in this section to generate a report of the record.
• Menu : Use the following menu to manage the record
  • Download Setting File : Click this button to download the setting file which contains variable values that have been used in the calculation of the record.
  • Delete : Click this button to delete the record before its expiration time.

Contact

If you found any problem persist in the system or would like to report a bug. Please contact: pitinat.asa@mahidol.ac.th