bammetrics

Accelerated GATK4 CollectWGSMetrics.

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.

Refer to the bammetrics 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 $(pwd):/outputdir \
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    --workdir /workdir \
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    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
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    pbrun bammetrics \
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    --ref /workdir/${REFERENCE_FILE} \
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    --bam /workdir/${INPUT_BAM} \
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    --out-metrics-file /outputdir/${METRICS_FILE}

Compatible GATK4 Command

The command below is the GATK4 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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$ gatk CollectWgsMetrics \
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    -R <INPUT_DIR>/${REFERENCE_FILE} \
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    -I <INPUT_DIR>/${INPUT_BAM} \
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    -O <OUTPUT_DIR>/${METRICS_FILE}

Options