> For clean Markdown of any page, append .md to the page URL.
> For a complete documentation index, see https://docs.nvidia.com/clara/parabricks/v4.7.1/tutorials/step-by-step-tutorials/llms.txt.
> For AI client integration (Claude Code, Cursor, etc.), connect to the MCP server at https://docs.nvidia.com/clara/parabricks/_mcp/server.

# Step-by-Step Tutorials

These tutorials walk you through a simple use case for NVIDIA Parabricks, giving a brief introduction to
how it works. We'll start by downloading some sample data:

* A reference file (`Homo_sapiens_assembly38.fasta`) and its index
* A 'known indels' file and its index
* Two FASTQ files
* Associated index files
* One BAM file for markdup
* One single-ended BAM file

The tutorials then walk through the following steps:

* Alignment (FASTA + FASTQ ==> BAM)
* Variant calling (FASTA + BAM ==> VCF)

These tutorials are meant to be simple and straightforward and to only cover a single, specific
use case. You should be able to copy and paste the commands into a terminal window and get
the same results as shown. The [Detailed Tutorials for Parabricks Pipelines](/tutorials/detailed-tutorials) cover more general problem solving using
Parabricks.

## Steps in the Tutorial

* [Getting the Sample Data](/tutorials/step-by-step-tutorials/getting-the-sample-data)
* [FQ2BAM Tutorial](/tutorials/step-by-step-tutorials/fq-2-bam-tutorial)
* [HaplotypeCaller Tutorial](/tutorials/step-by-step-tutorials/haplotype-caller-tutorial)

## Docs

- [Getting the Sample Data](https://docs.nvidia.com/clara/parabricks/v4.7.1/tutorials/step-by-step-tutorials/getting-the-sample-data.md): 
- [FQ2BAM Tutorial](https://docs.nvidia.com/clara/parabricks/v4.7.1/tutorials/step-by-step-tutorials/fq-2-bam-tutorial.md): 
- [HaplotypeCaller Tutorial](https://docs.nvidia.com/clara/parabricks/v4.7.1/tutorials/step-by-step-tutorials/haplotype-caller-tutorial.md):