> This page is for version v4.7.1.
> 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 `g.vcf`/`g.vcf.gz` files. The index file name is determined
by appending `.tbi` to the name of the GVCF file being indexed, and is created in the same directory
as the index file itself.

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 $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
    pbrun indexgvcf \
    --input /workdir/${INPUT_GVCF}
```

## Compatible CPU GATK4 Command

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

## Options