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Nvidia Clara Parabricks haplotypecaller

Logo for Nvidia Clara Parabricks haplotypecaller
Description
Run a GPU-accelerated haplotypecaller.
Publisher
Nvidia
Latest Tag
4.0.0-1
Modified
March 1, 2024
Compressed Size
92.95 MB
Multinode Support
No
Multi-Arch Support
No
4.0.0-1 (Latest) Security Scan Results

Linux / amd64

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This tool applies an accelerated GATK CollectMultipleMetrics for assessing the metrics of a BAM file, such as including alignment success, quality score distributions, GC bias, and sequencing artifacts. This functions as a ‘meta-metrics’ tool, and can run any combination of the available metrics tools in GATK to assess overall how well a sequencing run has performed. The available metrics tools (PROGRAMs) can be found in the command line example below.

You can provide an optional BQSR report to fix the BAM, similar to ApplyBQSR. In this case, the updated base qualities will be used.

For further information visit the haplotypecaller 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 haplotypecaller \
    --ref /workdir/${REFERENCE_FILE} \
    --in-bam /workdir/${INPUT_BAM} \
    --in-recal-file /workdir/${INPUT_RECAL_FILE} \
    --out-variants /outputdir/${OUTPUT_VCF}