bqsr
Performs Base Quality Score Recalibration (BQSR) in a standalone fashion.
$ pbrun bqsr \
--ref Ref/Homo_sapiens_assembly38.fasta \
--in-bam mark_dups_gpu.bam \
--knownSites Ref/Homo_sapiens_assembly38.known_indels.vcf.gz \
--out-recal-file recal_gpu.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.
$ gatk BaseRecalibrator --java-options -Xmx30g --input mark_dups_gpu.bam --output \
recal_cpu.txt --known-sites Ref/Homo_sapiens_assembly38.known_indels.vcf.gz \
--reference Ref/Homo_sapiens_assembly38.fasta
Run bqsr on a BAM file to generate a BQSR report.
Input/Output file options
- --ref REF
- --in-bam IN_BAM
- --knownSites KNOWNSITES
- --interval-file INTERVAL_FILE
- --out-recal-file OUT_RECAL_FILE
Path to the reference file. (default: None)
Option is required.
Path to the BAM file. (default: None)
Option is required.
Path to a known indels file. The file must be in vcf.gz format. This option can be used multiple times. (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 Report File. (default: None)
Option is required.
Tool Options:
- -L INTERVAL, --interval INTERVAL
- -ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING
Interval within which to call bqsr 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)
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.