> 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.

# genotypegvcf

This tool converts variant calls in g.vcf format to VCF format.

This tool applies an accelerated GATK GenotypeGVCFs for joint genotyping,
converting from `g.vcf` format to regular VCF format. This utilizes the HaplotypeCaller
genotype likelihoods, produced with the `-ERC` GVCF flag, to joint genotype on one
or more (multi-sample) `g.vcf` files.

Refer to the [genotypegvcf 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 $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
    pbrun genotypegvcf \
    --ref /workdir/${REFERENCE_FILE} \
    --in-gvcf /workdir/${INPUT_GVCF_FILE} \
    --out-vcf /outputdir/${OUTPUT_VCF}
```

## Compatible CPU GATK4 Command

```sh
$ gatk GenotypeGVCFs \
    -R <INPUT_DIR>/${REFERENCE_FILE} \
    -V <INPUT_DIR>/${INPUT_GVCF_FILE} \
    -O <OUTPUT_DIR>/${OUTPUT_VCF}
```

## Options