Table of contents
Allelica Modules User Guide
Impute App User Guide and Benchmark


Allelica supports users with a simple process to enrich Low Coverage WGS Data. This support is provided within Illumina's BaseSpace.

Prerequisites for Access to Impute

Allelica's Impute module runs through our App interface on third-party software. This means that you must first register at Illumina. Once you are logged into Illumina, you have access to the BaseSpace dashboard.

Illumina analyses genetic samples and provides users with input data (FASTQ). Illumina customers have access to BaseSpace. The results of your genetic analysis are uploaded on your BaseSpace account by Illumina. Once your FASTQ is available, you may select the biosample data to be analysed and use our pipeline to impute the data.

This guide will therefore assume that all users have completed their registration process and have their data loaded on the Illumina system.

Step 1 – Select the Data

1.1 Select the data that you wish to analyze by navigating from My Data > Projects on the top menu bar.

1.2 Select your sample from your dataset list using the checkbox.

Step 2 – Launch the App

2.1 Select "Launch App" from the internal top menu bar.

2.2 Select the Allelica App by navigating to "Allelica Impute - Low Coverage" from the App list.

Step 3 – Load your Data into the App

3.1 (Optional) Customize the name for your analysis run.

3.2 Click "Biosample" to identify the test sample from your list of samples.

Step 4 – Setup the Analyses

4.1 Choose the time run for your analyses.

The computational power required to run our algorithm is substantial. More computational power allows your data to be processed more efficiently. It is important to balance cost against the time available.

4.2 Click "Launch Application".

Depending on the number of samples, the application's response time may be measured in minutes.

4.3 Click "Accept" to allow the app to access your FASTQ and user information.

Step 5 – Receive your Results

Your results will be provided in VCF compressed format for each chromosome of each sample submitted. The results will be available in the "File" section of your project.


If you need assistance, please reach out.