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