bamsort - NVIDIA Docs

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.

See the bamsort Reference section for a detailed listing of all available options.

Quick Start

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            # 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 $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.7.0-1 \
    pbrun bamsort \
    --ref /workdir/${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. The output from this command will be identical to the output from the above command.

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            $ java -Xmx30g -jar picard.jar SortSam \
    I=<INPUT_DIR>/${INPUT_BAM} \
    O=<OUTPUT_DIR>/${OUTPUT_BAM}

bamsort Reference

Sort BAM files. There are five modes: Coordinate sort (Picard-compatible), Coordinate sort (fgbio-compatible), queryname sort (Picard-compatible), queryname sort (fgbio-compatible), and template coordinate sort (fgbio- compatible).

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 half of the total system memory. (default: 62)
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	`--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.