> 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.

# indexgvcf

This tool creates an index for a VCF(`vcf.gz`) or GVCF(`g.vcf`/`g.vcf.gz`) file. The index file name is determined
by appending `.tbi` to the name of the `vcf.gz`/`g.vcf.gz` file, or `.idx` to the name of the `g.vcf` file being indexed,
and is created in the same directory as the VCF/GVCF file itself.

Please note that [haplotypecaller](/clara/parabricks/v4.8.0/tool-reference/tools/haplotypecaller) and [deepvariant](/clara/parabricks/v4.8.0/tool-reference/tools/deepvariant)
also write the index file when generating a `.gz` output.

Refer to the [indexgvcf 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 $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1 \
    pbrun indexgvcf \
    --input /workdir/${INPUT_GVCF}
```

## Compatible CPU GATK4 Command

```sh
$ gatk IndexFeatureFile -I <INPUT_DIR>/${INPUT_GVCF}
```

## Options

| Type    | Name                                    | Required? | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| ------- | --------------------------------------- | --------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| I/O     | `--input INPUT`                         | Yes       | Path to the g.vcf/g.vcf.gz file to be indexed.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
| 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.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |