Clara Parabricks v3.7.0
3.7.0

bammetrics

Accelerated CollectWGSMetrics functionality from GATK4. bammetrics collects whole genome sequencing metrics, similar to CollectWGSMetrics from GATK4, but in a highly accelerated manner. The output metrics match exactly with that of GATK4.

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$ pbrun bammetrics \ --ref Ref.fa \ --bam wgs.bam \ --out-metrics-file metrics.txt

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 CollectWGSMetrics -R Ref.fa -I wgs.bam -O metrics.txt

Run bammetrics on a BAM file to generate metrics file.

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.

--interval-file INTERVAL_FILE

Path to an interval file with possible formats: Picard-style (.interval_list or .picard), GATK-style (.list or .intervals), or BED file (.bed). This option can be used multiple times. (default: None)

--out-metrics-file OUT_METRICS_FILE

Output Metrics File. (default: None)

Option is required.

Options specific to this tool

--minimum-base-quality MINIMUM_BASE_QUALITY

Minimum base quality for a base to contribute coverage. (default: 20)

--minimum-mapping-quality MINIMUM_MAPPING_QUALITY

Minimum mapping quality for a read to contribute coverage. (default: 20)

--count-unpaired

If true, count unpaired reads, and paired reads with one end unmapped. (default: None)

--coverage-cap COVERAGE_CAP

Treat positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED). (default: 250)

--num-threads NUM_THREADS

Number of threads to run. (default: 12)

-L INTERVAL, --interval INTERVAL

Interval within which to collect metrics from the BAM/CRAM file. All intervals will have a padding of 0 to get read records and overlapping intervals will be combined. Interval files should be passed using the --interval-file option. This option can be used multiple times. e.g. "-L chr1 -L chr2:10000 -L chr3:20000+ -L chr4:10000-20000". (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.

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