Linux / amd64
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.
# 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