> 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. # bamsort Sort BAM files. This tool can sort the reads within a BAM file in a variety of ways, including by position in the genome (coordinate) or read name (queryname). This enables compatibility with the requirements of different downstream tools. Five sort modes are supported: * coordinate (Picard-compatible) * coordinate (fgbio-compatible) * queryname (Picard-compatible) * queryname (fgbio-compatible) * template coordinate sort (fgbio-compatible) Allowed values for **--sort-order** are as follows: * coordinate \[default] * queryname * templatecoordinate Allowed values for **--sort-compatibility** are as follows: * picard \[default] * fgbio *coordinate* and *queryname* sorting can be done in either *picard* or *fgbio* mode. *templatecoordinate* can only be done in fgbio mode. Refer to the [bamsort 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 $(pwd):/outputdir \ --workdir /workdir \ nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1 \ pbrun bamsort \ --ref /workdir/${REFERENCE_FILE} \ --in-bam /workdir/${INPUT_BAM} \ --out-bam /outputdir/${OUTPUT_BAM} \ --sort-order coordinate ``` ## Compatible Picard Command The command below is the Picard counterpart of the Parabricks command above. This command will produce output equivalent to the output from the above command. ```sh $ java -Xmx30g -jar picard.jar SortSam \ I=/${INPUT_BAM} \ O=/${OUTPUT_BAM} \ SORT_ORDER=coordinate ``` ## Options | Type | Name | Required? | Description | | ----------- | ----------------------------------------------- | --------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | I/O | `--in-bam IN_BAM` | Yes | Path of BAM/CRAM for sorting. This option is required. | | I/O | `--out-bam OUT_BAM` | Yes | Path of BAM/CRAM file after sorting. | | I/O | `--ref REF` | Yes | Path to the reference file. | | Tool | `--sort-order SORT_ORDER` | No | Type of sort to be done. Possible values are \{coordinate,queryname,templatecoordinate}. (default: coordinate) | | Tool | `--sort-compatibility SORT_COMPATIBILITY` | No | Sort comparator compatibility to be used for compatibility with other tools. Possible values are \{picard,fgbio}. TemplateCoordinate will only use fgbio. (default: picard) | | Performance | `--num-zip-threads NUM_ZIP_THREADS` | No | Number of CPUs to use for zipping BAM files in a run (default 16 for coordinate sorts and 10 otherwise). | | Performance | `--num-sort-threads NUM_SORT_THREADS` | No | Number of CPUs to use for sorting in a run (default 10 for coordinate sorts and 16 otherwise). | | Performance | `--max-records-in-ram MAX_RECORDS_IN_RAM` | No | Maximum number of records in RAM when using a queryname or template coordinate sort mode; lowering this number will decrease maximum memory usage. (default: 65000000) | | Performance | `--mem-limit MEM_LIMIT` | No | Memory limit in GBs during sorting and postsorting. By default, the limit is 70% of the total system memory. | | Performance | `--gpuwrite` | No | Use one GPU to accelerate writing final BAM/CRAM. | | Performance | `--gpuwrite-deflate-algo GPUWRITE_DEFLATE_ALGO` | No | Choose the nvCOMP DEFLATE algorithm to use with --gpuwrite. Note these options do not correspond to CPU DEFLATE options. Valid options are 1, 2, and 4. Option 1 is fastest, while options 2 and 4 have progressively lower throughput but higher compression ratios. The default value is 1 when the user does not provide an input (i.e., None) | | Performance | `--gpusort` | No | Use GPUs to accelerate sorting and marking. | | 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. |