Tool ReferenceTools

collectmultiplemetrics

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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.

Refer to the collectmultiplemetrics Reference section for a detailed listing of all available options.

Quick Start

1# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
2docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
3    --workdir /workdir \
4    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
5    pbrun collectmultiplemetrics \
6    --ref /workdir/${REFERENCE_FILE} \
7    --bam /workdir/${INPUT_BAM} \
8    --out-qc-metrics-dir /outputdir/${OUTPUT_DIR}\
9    --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.

1$ gatk CollectMultipleMetrics \
2--REFERENCE_SEQUENCE <INPUT_DIR>/${REFERENCE_FILE} \
3-I <INPUT_DIR>/${INPUT_BAM} \
4-O <OUTPUT_DIR>/${OUTPUT_DIR} \
5--PROGRAM CollectAlignmentSummaryMetrics \
6--PROGRAM CollectInsertSizeMetrics \
7--PROGRAM QualityScoreDistribution \
8--PROGRAM MeanQualityByCycle \
9--PROGRAM CollectBaseDistributionByCycle \
10--PROGRAM CollectGcBiasMetrics \
11--PROGRAM CollectSequencingArtifactMetrics \
12--PROGRAM CollectQualityYieldMetrics

Options

TypeNameRequired?Description
I/O--ref REFYesPath to the reference file.
I/O--bam BAMYesPath to the BAM file.
I/O--out-qc-metrics-dir OUT_QC_METRICS_DIRYesOutput Directory to store results of each analysis.
Tool--gen-all-metricsNoGenerate QC for every analysis.
Tool--gen-alignmentNoGenerate QC for alignment summary metric.
Tool--gen-quality-scoreNoGenerate QC for quality score distribution metric.
Tool--gen-insert-sizeNoGenerate QC for insert size metric.
Tool--gen-mean-quality-by-cycleNoGenerate QC for mean quality by cycle metric.
Tool--gen-base-distribution-by-cycleNoGenerate QC for base distribution by cycle metric.
Tool--gen-gc-biasNoPrefix name used to generate detail and summary files for gc bias metric.
Tool--gen-seq-artifactNoGenerate QC for sequencing artifact metric.
Tool--gen-quality-yieldNoGenerate QC for quality yield metric.
Performance--bam-decompressor-threads BAM_DECOMPRESSOR_THREADSNoNumber of threads for BAM decompression. (default: 3)
Runtime--verboseNoEnable verbose output.
Runtime--x3NoShow full command line arguments.
Runtime--logfile LOGFILENoPath to the log file. If not specified, messages will only be written to the standard error output.
Runtime--tmp-dir TMP_DIRNoFull path to the directory where temporary files will be stored. (default: .)
Runtime--with-petagene-dir WITH_PETAGENE_DIRNoFull 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-tmpNoDo not delete the directory storing temporary files after completion.
Runtime--no-seccomp-overrideNoDo not override seccomp options for docker.
Runtime--versionNoView compatible software versions.
Runtime--preserve-file-symlinksNoOverride default behavior to keep file symlinks intact and *not* resolve the symlink.
Runtime--num-gpus NUM_GPUSNoNumber of GPUs to use for a run. (default: 1)