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.

See the applybqsr Reference section for a detailed listing of all available options.

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 \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1 \
    pbrun applybqsr \
    --ref /workdir/${REFERENCE_FILE} \
    --in-bam /workdir/${INPUT_BAM} \
    --in-recal-file /workdir/${INPUT_RECAL_FILE}  \
    --out-bam /outputdir/${OUTPUT_BAM}

Compatible GATK4 Command

The command below is the GATK4 counterpart of the Parabricks command above. The output from these commands will be identical to the output from the above command.

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            $ 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}

applybqsr Reference

Update the Base Quality Scores using the 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.

--in-recal-file IN_RECAL_FILE

Path to the BQSR report 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-bam OUT_BAM

Output BAM file. (default: None)

Option is required.

Tool Options:

-L INTERVAL, --interval INTERVAL: 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)
-ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING: Amount of padding (in base pairs) to add to each interval you are including. (default: None)

Performance Options:

--num-threads NUM_THREADS: Number of threads for worker. (default: 8)

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.

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