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

# prepon

Generate an index for a PON file. This is a prerequisite for using the "--pon" option in [mutectcaller](/tool-reference/tools/mutectcaller).

`prepon` requires that the Contig field be present in the header of the input `.vcf.gz` file in order to do
memory allocation at the start of execution. This field should include both the chromosome name and length:

```text
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
...
```

If your input `.vcf.gz` file does not include these value, run this command to update the header before running `prepon`:

```bash
$ bcftools reheader --fai YOUR_REFERENCE_FILE.fa.fai INPUT_PON.vcf.gz > UPDATED_PON.vcf.gz
```

Refer to the [prepon Reference](#options) section for a detailed listing of all available options.

## Quick Start

```sh
# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
    pbrun prepon \
    --in-pon-file /workdir/${INPUT_PON_VCF}
```

## Options