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 section for a detailed listing of all available options.

Quick Start

# 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.

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

Options