Accelerated CollectMultipleMetrics from GATK4. collectmultiplemetrics collects whole genome sequencing metrics, similar to CollectMultipleMetrics from GATK4, but in a highly accelerated manner. The output metrics match exactly those of GATK4.


$ pbrun collectmultiplemetrics \ --ref Ref.fa \ --bam wgs.bam \ --out-qc-metrics-dir output-qc\ --gen-all-metrics

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.


gatk CollectMultipleMetrics \ --REFERENCE_SEQUENCE Ref.fa -I wgs.bam -O metrics \ --PROGRAM CollectAlignmentSummaryMetrics \ --PROGRAM CollectInsertSizeMetrics \ --PROGRAM QualityScoreDistribution \ --PROGRAM MeanQualityByCycle \ --PROGRAM CollectBaseDistributionByCycle \ --PROGRAM CollectGcBiasMetrics \ --PROGRAM CollectSequencingArtifactMetrics \ --PROGRAM CollectQualityYieldMetrics

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

Input/Output file options

--ref REF

Path to the reference file. (default: None)

Option is required.

--bam BAM

Path to the BAM file. (default: None)

Option is required.

--out-qc-metrics-dir OUT_QC_METRICS_DIR

Output Directory to store results of each analysis.

(default: None)

Option is required.

Options specific to this tool

--bam-decompressor-threads BAM_DECOMPRESSOR_THREADS

Number of threads for BAM decompression. (default: 3)


Generate QC for every analysis. (default: None)


Generate QC for alignment summary metric. (default: None)


Generate QC for quality score distribution metric. (default: None)


Generate QC for insert size metric. (default: None)


Generate QC for mean quality by cycle metric. (default: None)


Generate QC for base distribution by cycle metric. (default: None)


Prefix name used to generate detail and summary files for gc bias metric. (default: None)


Generate QC for sequencing artifact metric. (default: None)


Generate QC for quality yield metric. (default: None)

Common options:

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

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 (default: None)


Do not delete the directory storing temporary files after completion.

--license-file LICENSE_FILE

Path to license file license.bin if not in the installation directory.


Do not override seccomp options for docker (default: None).


View compatible software versions.

GPU options:

--num-gpus NUM_GPUS

Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.

--gpu-devices GPU_DEVICES

GPU devices to use for a run. By default, all GPU devices will be used. To use specific GPU devices, enter a comma-separated list of GPU device numbers. Possible device numbers can be found by examining the output of the nvidia-smi command. For example, using --gpu-devices 0,1 would only use the first two GPUs.

© Copyright 2022, Nvidia. Last updated on Jun 28, 2023.