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Nvidia Clara Parabricks bammetrics

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Description

Accelerated GATK4 CollectWGSMetrics.

Publisher

Nvidia

Latest Tag

4.0.0-1

Modified

November 1, 2022

Compressed Size

89.16 MB

Multinode Support

No

Multi-Arch Support

No

4.0.0-1 (Latest) Scan Results

Linux / amd64

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 \
    nvcr.io/nvidia/clara/clara-parabricks:<VERSION-TAG> \
    pbrun bammetrics \
    --ref /workdir/${REFERENCE_FILE} \
    --bam /workdir/${INPUT_BAM} \
    --out-metrics-file /outputdir/${METRICS_FILE}