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bqsr

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This tool generates a Base Quality Score Recalibration report, which can be applied by the applybqsr tool, to recalibrate the quality scores in a BAM file. This is applied as part of the recommended GATK best practices to maximize accuracy in variant calling.

Refer to the bqsr Reference section for a detailed listing of all available options.

Quick Start

# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
     --workdir /workdir \
     nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1 \
     pbrun bqsr \
     --ref /workdir/${REFERENCE_FILE} \
     --in-bam /workdir/${INPUT_BAM} \
     --knownSites /workdir/${KNOWN_SITES_FILE} \
     --out-recal-file /outputdir/${INPUT_RECAL_FILE}

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 BaseRecalibrator \
    --java-options -Xmx30g \
    --input <INPUT_DIR>/${INPUT_BAM} \
    --output <OUTPUT_DIR>/${INPUT_RECAL_FILE} \
    --known-sites <INPUT_DIR>/${KNOWN_SITES_FILE} \
    --reference <INPUT_DIR>/${REFERENCE_FILE}

Options

TypeNameRequired?Description
I/O--ref REFYesPath to the reference file.
I/O--in-bam IN_BAMYesPath to the BAM file.
I/O--knownSites KNOWNSITESYesPath to a database of known polymorphic sites used to exclude regions around known polymorphisms from analysis. The file can be in vcf or vcf.gz format. This option can be used multiple times.
I/O--interval-file INTERVAL_FILENoPath 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.
I/O--out-recal-file OUT_RECAL_FILEYesOutput Report File.
Tool-L INTERVAL, --interval INTERVALNoInterval 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").
Tool-ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDINGNoAmount of padding (in base pairs) to add to each interval you are including.
Runtime--verboseNoEnable verbose output.
Runtime--x3NoShow full command line arguments.
Runtime--dry-runNoCheck if the current command is valid.
Runtime--logfile LOGFILENoPath to the log file. If not specified, messages will only be written to the standard error output.
Runtime--tmp-dir TMP_DIRNoFull path to the directory where temporary files will be stored. (default: .)
Runtime--with-petagene-dir WITH_PETAGENE_DIRNoFull 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. Optionally set the PetaLinkMode environment variable that is used to further configure PetaLink, notably setting it to "+write" to enable outputting compressed BAM and .fastq files.
Runtime--keep-tmpNoDo not delete the directory storing temporary files after completion.
Runtime--no-seccomp-overrideNoDo not override seccomp options for docker.
Runtime--versionNoView compatible software versions.
Runtime--preserve-file-symlinksNoOverride default behavior to keep file symlinks intact and *not* resolve the symlink.
Runtime--help-jsonNoPrint out help message in JSON format.
Runtime--num-gpus NUM_GPUSNoNumber of GPUs to use for a run. (default: 1)