> This page is for version v4.8.0 (default).
> For other versions, use one of these documentation indexes:
> - v4.8.0 (default): https://docs.nvidia.com/clara/parabricks/v4.8.0/llms.txt
> - v4.7.1: https://docs.nvidia.com/clara/parabricks/v4.7.1/llms.txt

> 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](/clara/parabricks/v4.8.0/tool-reference/tools/mutectcaller).

The PON file needs to be a bgzip-compressed `vcf.gz` file.

`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 values, run this command to update the header before running `prepon`:

```bash
docker run --rm --volume $(pwd):/workdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1 \
    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 $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1 \
    pbrun prepon \
    --in-pon-file /workdir/${INPUT_PON_VCF_GZ}
```

## Options

| Type    | Name                                    | Required? | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| ------- | --------------------------------------- | --------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| I/O     | `--in-pon-file IN_PON_FILE`             | Yes       | Path to the input PON file in vcf.gz format with its tabix index.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| Runtime | `--verbose`                             | No        | Enable verbose output.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
| Runtime | `--x3`                                  | No        | Show full command line arguments.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| Runtime | `--dry-run`                             | No        | Check if the current command is valid.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
| Runtime | `--logfile LOGFILE`                     | No        | Path to the log file. If not specified, messages will only be written to the standard error output.                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
| Runtime | `--tmp-dir TMP_DIR`                     | No        | Full path to the directory where temporary files will be stored. (default: .)                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
| Runtime | `--with-petagene-dir WITH_PETAGENE_DIR` | No        | Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials. Optionally set the PetaLinkMode environment variable that is used to further configure PetaLink, notably setting it to "+write" to enable outputting compressed BAM and .fastq files. |
| Runtime | `--keep-tmp`                            | No        | Do not delete the directory storing temporary files after completion.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| Runtime | `--no-seccomp-override`                 | No        | Do not override seccomp options for docker.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| Runtime | `--version`                             | No        | View compatible software versions.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
| Runtime | `--preserve-file-symlinks`              | No        | Override default behavior to keep file symlinks intact and *not* resolve the symlink.                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| Runtime | `--help-json`                           | No        | Print out help message in JSON format.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
| Runtime | `--num-gpus NUM_GPUS`                   | No        | Number of GPUs to use for a run. (default: 1)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |