Input Requirements

Before submitting a job, ensure that your input cram manifest meets these conditions:

• has 3 columns with these headers: sample_id, cram_path, cram_index_path
• counts of CRAMs, CRAIs, and sample IDs match
• sample IDs are unique
• CRAM paths are unique
• CRAM file names end with .cram and indices end with .crai
• CRAM and CRAI paths use gs:// format and are accessible to both the submitter and service (see Cloud Inputs for instructions)

Also ensure that for each of the cram files in the manifest:

• CRAM file sizes do not exceed 10 GB
• CRAM files are aligned to the hg38 reference genome
• CRAM has data across the genome

The service will check that your inputs meet the above requirements and will return a relevant error message explaining which requirements are not met.

For a deeper dive into the pipeline, please see Pipeline Overview

If you experience errors, check our Troubleshooting page.