# Advanced Topics

## CRAM Input

When CRAM is used as input and the reference genome used to compress the CRAM files differs from the reference genome used for the analysis, the CRAM reference genome must be provided using the [custom configuration file](/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/installation/advanced/custom_config.md).


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/installation/advanced.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.