bammetrics

NVIDIA Docs Hub NVIDIA Clara NVIDIA Parabricks (4.2.1) 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.

Quick Start

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            # 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 \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.2.1-1 \
    pbrun bammetrics \
    --ref /workdir/${REFERENCE_FILE} \
    --bam /workdir/${INPUT_BAM} \
    --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 \
    -R <INPUT_DIR>/${REFERENCE_FILE} \
    -I <INPUT_DIR>/${INPUT_BAM} \
    -O <OUTPUT_DIR>/${METRICS_FILE}

bammetrics Reference

Run bammetrics on a BAM file to generate a metrics file.

Input/Output file options

--ref REF
--bam BAM
--interval-file INTERVAL_FILE
--out-metrics-file OUT_METRICS_FILE

Tool Options:

--minimum-base-quality MINIMUM_BASE_QUALITY
--minimum-mapping-quality MINIMUM_MAPPING_QUALITY
--count-unpaired
--coverage-cap COVERAGE_CAP
-L INTERVAL, --interval INTERVAL

Performance Options:

--num-threads NUM_THREADS

Common options:

--logfile LOGFILE
--tmp-dir TMP_DIR
--with-petagene-dir WITH_PETAGENE_DIR
--keep-tmp
--no-seccomp-override
--version