CRAMs

Enabling uploads

To enable CRAM uploads request access to Gencove Support. You can expect a response within 1 business day.

For CRAM files the only available method for uploading is via S3 Integration.

Restrictions

CRAM files have already been aligned against a reference genome and should be used with a pipeline configuration that has a matching reference genome. See how to create a project and available pipeline configurations.

Our system validates that the pipeline reference genome and the CRAM reference genome are the same. If this validation doesn't succeed we mark the sample as "Failed QC".

Naming conventions

By default we look for SM: headers in your CRAM files to identify the sample id.

For this you need to provide both CRAM and CRAI (index) files so we can quickly look up this information before starting to import and process your files. Example files: sample1.cram and sample1.cram.crai.