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.
$ 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
- --bam BAM
- --out-qc-metrics-dir OUT_QC_METRICS_DIR
Path to the reference file. (default: None)
Option is required.
Path to the BAM file. (default: None)
Option is required.
Output Directory to store results of each analysis.
(default: None)
Option is required.
Tool Options:
- --bam-decompressor-threads BAM_DECOMPRESSOR_THREADS
- --gen-all-metrics
- --gen-alignment
- --gen-quality-score
- --gen-insert-size
- --gen-mean-quality-by-cycle
- --gen-base-distribution-by-cycle
- --gen-gc-bias
- --gen-seq-artifact
- --gen-quality-yield
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
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --no-seccomp-override
- --version
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
Full path to the directory where temporary files will be stored.
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.
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
- --gpu-devices GPU_DEVICES
Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.
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.