Uploading samples
GeneBe Sample Analysis is an early-access workflow for analysing genomic samples in the web application.
The upload and analysis flow is still evolving. Use the options shown in the application for the currently supported requirements. Daily upload limits are described below.
Supported input
- VCF files for variant-focused analysis.
- FASTQ files for raw sequencing reads.
- BAM files for aligned reads.
For read-based uploads, GeneBe may ask for a target-region BED file. For trio analysis, provide or link data for the child, mother, and father as prompted by the application.
Before you upload
- Confirm that the file belongs to the intended sample or case.
- Select the correct genome build when the application asks for it.
- Do not upload data unless you are authorized to process it in GeneBe.
- Check that you have not used up your daily upload limit.
Daily upload limits
The number of samples you can upload per day depends on your account plan: 3 for a logged-in user (Small), 10 for Moderate and 100 for Large. You need to be logged in to upload samples. After exceeding the limit, the upload is rejected with 429 Too Many Requests and a description of the problem.
This limit is independent of the daily limit of annotated variants. Variants in uploaded samples count towards the variants limit too, so hitting it may prevent a whole sample from being annotated. See Rate Limits for the full list of limits.
Prefer to script it? You can create a sample, upload a VCF, and fetch the annotated result with GeneBeClient or the API: see Annotate a whole sample.
After analysis, you can filter the results and prepare a report. See Reports and templates.