bammetrics
Accelerated GATK4 CollectWGSMetrics.
This tool applies an accelerated version of the GATK CollectWGSMetrics for assessing coverage and quality of an aligned whole-genome BAM file. This includes metrics such as the fraction of reads that pass the base and mapping quality filters, and the coverage levels (read-depth) across the genome. These act as an overall quality check for the user, allowing assessment of how well a sequencing run has performed.
See the bammetrics Reference section for a detailed listing of all available options.
# This command assumes all the inputs are in INPUT_DIR and all the outputs go to OUTPUT_DIR.
docker run --rm --gpus all --volume INPUT_DIR:/workdir --volume OUTPUT_DIR:/outputdir \
--workdir /workdir \
nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1 \
pbrun bammetrics \
--ref /workdir/${REFERENCE_FILE} \
--bam /workdir/${INPUT_BAM} \
--out-metrics-file /outputdir/${METRICS_FILE}
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 <INPUT_DIR>/${REFERENCE_FILE} \
-I <INPUT_DIR>/${INPUT_BAM} \
-O <OUTPUT_DIR>/${METRICS_FILE}
Run bammetrics on a BAM file to generate a 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 in one of these 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.
Tool Options:
- --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)
- -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)
Performance Options:
- --num-threads NUM_THREADS
-
Number of threads to run. (default: 12)
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.
- --no-seccomp-override
-
Do not override seccomp options for docker (default: None).
- --version
-
View compatible software versions.