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Nvidia Clara Parabricks bammetrics

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Accelerated GATK4 CollectWGSMetrics.
Latest Tag
April 1, 2024
Compressed Size
89.16 MB
Multinode Support
Multi-Arch Support
4.0.0-1 (Latest) Security Scan Results

Linux / amd64

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This tool applies an accelerated version of the GATK CollectWGSMetrics for assessing coverage and quality of an aligned whole-genome BAM file. This includes metrics such as the fraction of reads that pass the base and mapping quality filters, and the coverage levels (read-depth) across the genome. These act as an overall quality check for the user, allowing assessment of how well a sequencing run has performed.

or further information visit the bammetrics 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 \<VERSION-TAG> \
    pbrun bammetrics \
    --ref /workdir/${REFERENCE_FILE} \
    --bam /workdir/${INPUT_BAM} \
    --out-metrics-file /outputdir/${METRICS_FILE}