> 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.

# bqsr

This tool generates a Base Quality Score Recalibration report, which can be
applied by the [applybqsr](/tool-reference/tools/applybqsr) tool, to recalibrate the quality scores in a BAM
file. This is applied as part of the recommended GATK best practices to
maximize accuracy in variant calling.

Refer to the [bqsr 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 $(pwd):/outputdir \
     --workdir /workdir \
     nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
     pbrun bqsr \
     --ref /workdir/${REFERENCE_FILE} \
     --in-bam /workdir/${INPUT_BAM} \
     --knownSites /workdir/${KNOWN_SITES_FILE} \
     --out-recal-file /outputdir/${INPUT_RECAL_FILE} \
```

## Compatible GATK4 Command

The command below is the GATK4 counterpart of the Parabricks command above. The output
from this command will be identical to the output from the above command.

```sh
$ gatk BaseRecalibrator \
    --java-options -Xmx30g \
    --input <INPUT_DIR>/${INPUT_BAM} \
    --output <OUTPUT_DIR>/${INPUT_RECAL_FILE} \
    --known-sites <INPUT_DIR>/${KNOWN_SITES_FILE} \
    --reference <INPUT_DIR>/${REFERENCE_FILE}
```

## Options