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.
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.
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.
3.1 (Optional) Customize the name for your analysis run.
3.2 Click "Biosample" to identify the test sample from your list of samples.
4.1 Choose the time run for your analyses.
4.2 Click "Launch Application".
4.3 Click "Accept" to allow the app to access your FASTQ and user information.
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.