collectmultiplemetrics

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.

Quick Start

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

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

collectmultiplemetrics Reference

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.

Tool Options:

--bam-decompressor-threads BAM_DECOMPRESSOR_THREADS

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

--gen-all-metrics

Generate QC for every analysis. (default: None)

--gen-alignment

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

--gen-quality-score

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

--gen-insert-size

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

--gen-mean-quality-by-cycle

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

--gen-base-distribution-by-cycle

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

--gen-gc-bias

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

--gen-seq-artifact

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

--gen-quality-yield

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)

--keep-tmp

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.

--no-seccomp-override

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

--version

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.