collectmultiplemetrics

Run a GPU-accelerated version of GATK’s CollectMultipleMetrics.

This tool applies an accelerated version of the GATK CollectMultipleMetrics for assessing BAM file metrics such as alignment success, quality score distributions, GC bias, and sequencing artifacts. This functions as a ‘meta-metrics’ tool that can run any combination of the available metrics tools in GATK to perform an overall assessment of how well a sequencing run has been performed. The available metrics tools (PROGRAMs) can be found in the reference section below.

See the collectmultiplemetrics 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.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.5.1-1 \
    pbrun collectmultiplemetrics \
    --ref /workdir/${REFERENCE_FILE} \
    --bam /workdir/${INPUT_BAM} \
    --out-qc-metrics-dir /outputdir/${OUTPUT_DIR}\
    --gen-all-metrics

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 CollectMultipleMetrics \
--REFERENCE_SEQUENCE <INPUT_DIR>/${REFERENCE_FILE} \
-I <INPUT_DIR>/${INPUT_BAM} \
-O <OUTPUT_DIR>/${OUTPUT_DIR} \
--PROGRAM CollectAlignmentSummaryMetrics \
--PROGRAM CollectInsertSizeMetrics \
--PROGRAM QualityScoreDistribution \
--PROGRAM MeanQualityByCycle \
--PROGRAM CollectBaseDistributionByCycle \
--PROGRAM CollectGcBiasMetrics \
--PROGRAM CollectSequencingArtifactMetrics \
--PROGRAM CollectQualityYieldMetrics

collectmultiplemetrics Reference

Run collectmultiplemetrics on a BAM file to generate files for multiple classes of metrics.

Type	Name	Required?	Description
I/O	‑‑ref REF	Yes	Path to the reference file.
I/O	‑‑bam BAM	Yes	Path to the BAM file.
I/O	‑‑out‑qc‑metrics‑dir OUT_QC_METRICS_DIR	Yes	Output Directory to store results of each analysis.
Tool	‑‑gen‑all‑metrics	No	Generate QC for every analysis.
Tool	‑‑gen‑alignment	No	Generate QC for alignment summary metric.
Tool	‑‑gen‑quality‑score	No	Generate QC for quality score distribution metric.
Tool	‑‑gen‑insert‑size	No	Generate QC for insert size metric.
Tool	‑‑gen‑mean‑quality‑by‑cycle	No	Generate QC for mean quality by cycle metric.
Tool	‑‑gen‑base‑distribution‑by‑cycle	No	Generate QC for base distribution by cycle metric.
Tool	‑‑gen‑gc‑bias	No	Prefix name used to generate detail and summary files for gc bias metric.
Tool	‑‑gen‑seq‑artifact	No	Generate QC for sequencing artifact metric.
Tool	‑‑gen‑quality‑yield	No	Generate QC for quality yield metric.
Performance	‑‑bam‑decompressor‑threads BAM_DECOMPRESSOR_THREADS	No	Number of threads for BAM decompression. (default: 3)
Runtime	‑‑verbose	No	Enable verbose output.
Runtime	‑‑x3	No	Show full command line arguments.
Runtime	‑‑logfile LOGFILE	No	Path to the log file. If not specified, messages will only be written to the standard error output.
Runtime	‑‑tmp‑dir TMP_DIR	No	Full path to the directory where temporary files will be stored. (default: .)
Runtime	‑‑with‑petagene‑dir WITH_PETAGENE_DIR	No	Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials. Optionally set the PetaLinkMode environment variable that is used to further configure PetaLink, notably setting it to "+write" to enable outputting compressed BAM and .fastq files.
Runtime	‑‑keep‑tmp	No	Do not delete the directory storing temporary files after completion.
Runtime	‑‑no‑seccomp‑override	No	Do not override seccomp options for docker.
Runtime	‑‑version	No	View compatible software versions.
Runtime	‑‑num‑gpus NUM_GPUS	No	Number of GPUs to use for a run. (default: 1)