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bqsr

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.

Quick Start

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            # 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
    -w /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:v4.0.1-1 \
    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.

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            $ 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}

bqsr Reference

Run bqsr on a BAM file to generate a BQSR report.

Input/Output file options

--ref REF

Path to the reference file. (default: None)

Option is required.

--in-bam IN_BAM

Path to the BAM file. (default: None)

Option is required.

--knownSites KNOWNSITES

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.

--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-recal-file OUT_RECAL_FILE

Output Report File. (default: None)

Option is required.

Tool Options:

-L INTERVAL, --interval INTERVAL: 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)
-ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING: Amount of padding (in base pairs) to add to each interval you are including. (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.
--no-seccomp-override: Do not override seccomp options for docker (default: None).
--version: 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.