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Nvidia Clara Parabricks collectmultiplemetrics

Logo for Nvidia Clara Parabricks collectmultiplemetrics
Description
Run a GPU-accelerated version of GATK’s CollectMultipleMetrics.
Publisher
Nvidia
Latest Tag
4.0.0-1
Modified
March 1, 2024
Compressed Size
161.63 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 version of the GATK CollectMultipleMetrics for assessing BAM file metrics such as alignment success, quality score distributions, GC bias, and sequencing artifacts. This functions as a ‘meta-metrics’ tool that can run any combination of the available metrics tools in GATK to perform an overall assessment of how well a sequencing run has been performed. The available metrics tools (PROGRAMs) can be found on the help page.

For further information visit the collectmultiplemetrics 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 collectmultiplemetrics \
    --ref /workdir/${REFERENCE_FILE} \
    --bam /workdir/${INPUT_BAM} \
    --out-qc-metrics-dir /outputdir/${OUTPUT_DIR}\
    --gen-all-metrics