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

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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.
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docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
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    --workdir /workdir \
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    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
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    pbrun bamsort \
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    --ref /workdir/${REFERENCE_FILE} \
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    --in-bam /workdir/${INPUT_BAM} \
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    --out-bam /outputdir/${OUTPUT_BAM} \
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    --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 \
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    I=<INPUT_DIR>/${INPUT_BAM} \
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    O=<OUTPUT_DIR>/${OUTPUT_BAM}

Options