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.

For further information visit the bamsort help page.

Quick Start

# This command assumes all the inputs are in <INPUT_DIR> and all the outputs go to <OUTPUT_DIR>.
$ docker run --rm --gpus all --volume <INPUT_DIR>:/workdir --volume <OUTPUT_DIR>:/outputdir
    -w /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:<VERSION-TAG> \
    pbrun bamsort \
    --ref /workdir/${REFERENCE_FILE} \
    --in-bam /workdir/${INPUT_BAM} \
    --out-bam /outputdir/${OUTPUT_BAM} \
    --sort-order coordinate