> 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. # bammetrics Accelerated GATK4 CollectWGSMetrics. This tool applies an accelerated version of the GATK CollectWGSMetrics for assessing coverage and quality of an aligned whole-genome BAM file. This includes metrics such as the fraction of reads that pass the base and mapping quality filters, and the coverage levels (read-depth) across the genome. These act as an overall quality check for the user, allowing assessment of how well a sequencing run has performed. Refer to the [bammetrics 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 $(pwd):/outputdir \ --workdir /workdir \ nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1 \ pbrun bammetrics \ --ref /workdir/${REFERENCE_FILE} \ --bam /workdir/${INPUT_BAM} \ --out-metrics-file /outputdir/${METRICS_FILE} ``` ## Compatible GATK4 Command The command below is the GATK4 counterpart of the Parabricks command above. The output from this command will be equivalent to the output from the above command. ```sh $ gatk CollectWgsMetrics \ -R /${REFERENCE_FILE} \ -I /${INPUT_BAM} \ -O /${METRICS_FILE} ``` ## Options | Type | Name | Required? | Description | | ----------- | --------------------------------------------------- | --------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | I/O | `--ref REF` | Yes | Path to the reference file. | | I/O | `--bam BAM` | Yes | Path to the BAM 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-metrics-file OUT_METRICS_FILE` | Yes | Output Metrics File. | | Tool | `--minimum-base-quality MINIMUM_BASE_QUALITY` | No | Minimum base quality for a base to contribute coverage. (default: 20) | | Tool | `--minimum-mapping-quality MINIMUM_MAPPING_QUALITY` | No | Minimum mapping quality for a read to contribute coverage. (default: 20) | | Tool | `--count-unpaired` | No | If specified, count unpaired reads and paired reads with one end unmapped. | | Tool | `--coverage-cap COVERAGE_CAP` | No | Treat positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED). (default: 250) | | Tool | `-L INTERVAL, --interval INTERVAL` | No | Interval within which to collect metrics from the BAM/CRAM file. All intervals will have a padding of 0 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"). | | Performance | `--num-threads NUM_THREADS` | No | Number of threads to run. (default: 12) | | 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. |