> 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. # applybqsr Updates the Base Quality Scores using the BQSR report. This tool recalibrates quality scores in a BAM file using the report generated by the [bqsr](/clara/parabricks/v4.8.0/tool-reference/tools/bqsr) tool. This should be applied after alignment but before variant calling to maximize final accuracy in variant calling, as recommended by GATK best practices. Note that the **applybqsr** tool will use at most two GPUs. Refer to the [applybqsr 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 $(pwd):/outputdir \ --workdir /workdir \ nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1 \ pbrun applybqsr \ --ref /workdir/${REFERENCE_FILE} \ --in-bam /workdir/${INPUT_BAM} \ --in-recal-file /workdir/${INPUT_RECAL_FILE} \ --out-bam /outputdir/${OUTPUT_BAM} ``` ## Compatible GATK4 Command The command below is the GATK4 counterpart of the Parabricks command above. The output from these commands will be equivalent to the output from the above command. ```sh $ gatk ApplyBQSR \ --java-options -Xmx30g \ -R /${REFERENCE_FILE} \ -I /${INPUT_BAM} \ --bqsr-recal-file /${INPUT_RECAL_FILE} \ -O /${OUTPUT_BAM} ``` ## Options | Type | Name | Required? | Description | | ----------- | ----------------------------------------------------------- | --------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | I/O | `--ref REF` | Yes | Path to the reference file. | | I/O | `--in-bam IN_BAM` | Yes | Path to the input BAM/CRAM file. | | I/O | `--in-recal-file IN_RECAL_FILE` | Yes | Path to the BQSR report file. | | I/O | `--interval-file INTERVAL_FILE` | No | Path to an interval file in one of these formats: Picard-style (.interval_list or .picard), GATK-style (.list or .intervals), or BED file (.bed). This option can be used multiple times. | | I/O | `--out-bam OUT_BAM` | Yes | Path to the output BAM/CRAM file. | | Tool | `-L INTERVAL, --interval INTERVAL` | No | Interval within which to call applyBQSR from the input reads. All intervals will have a padding of 100 to get read records, and overlapping intervals will be combined. Interval files should be passed using the --interval-file option. This option can be used multiple times (e.g. "-L chr1 -L chr2:10000 -L chr3:20000+ -L chr4:10000-20000"). | | Tool | `-ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING` | No | Amount of padding (in base pairs) to add to each interval you are including. | | Performance | `--num-threads NUM_THREADS` | No | Number of threads for worker. (default: 8) | | 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) |