applybqsr
Updates the Base Quality Scores using the BQSR report.
This tool recalibrates quality scores in a BAM file using the report generated by the bqsr [link] tool. This should be applied after alignment but before variant calling to maximize final accuracy in variant calling, as recommended by GATK best practices.
Please note that the applybqsr tool will use at most two GPUs.
# 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:4.1.1-1 \
pbrun applybqsr \
--ref /workdir/${REFERENCE_FILE} \
--in-bam /workdir/${INPUT_BAM} \
--in-recal-file /workdir/${INPUT_RECAL_FILE} \
--out-bam /outputdir/${OUTPUT_BAM}
The command below is the GATK4 counterpart of the Clara Parabricks command above. The output from these commands will be identical to the output from the above command.
$ gatk ApplyBQSR \
--java-options -Xmx30g \
-R <INPUT_DIR>/${REFERENCE_FILE} \
-I <INPUT_DIR>/${INPUT_BAM} \
--bqsr-recal-file <INPUT_DIR>/${INPUT_RECAL_FILE} \
-O <OUTPUT_DIR>/${OUTPUT_BAM}
Update the Base Quality Scores using the BQSR report.
Input/Output file options
- --ref REF
- --in-bam IN_BAM
- --in-recal-file IN_RECAL_FILE
- --interval-file INTERVAL_FILE
- --out-bam OUT_BAM
Path to the reference file. (default: None)
Option is required.
Path to the BAM file. (default: None)
Option is required.
Path to the bqsr report file. (default: None)
Option is required.
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)
Output BAM file. (default: None)
Option is required.
Tool Options:
- -L INTERVAL, --interval INTERVAL
- -ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING
- --num-threads NUM_THREADS
Interval within which to call applyBQSR from the input reads. All intervals will have a padding of 100 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)
Amount of padding (in base pairs) to add to each interval you are including. (default: None)
Number of threads for worker. (default: 8)
Common options:
- --logfile LOGFILE
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --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.
Do not override seccomp options for docker (default: None).
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.