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.

Quick Start

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

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

bammetrics Reference

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.