applybqsr - NVIDIA Docs

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.

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:4.2.1-1 \
    pbrun applybqsr \
    --ref /workdir/${REFERENCE_FILE} \
    --in-bam /workdir/${INPUT_BAM} \
    --in-recal-file /workdir/${INPUT_RECAL_FILE}  \
    --out-bam /outputdir/${OUTPUT_BAM}

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
--in-bam IN_BAM
--in-recal-file IN_RECAL_FILE
--interval-file INTERVAL_FILE
--out-bam OUT_BAM

Tool Options:

-L INTERVAL, --interval INTERVAL
-ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING

Performance Options:

--num-threads NUM_THREADS

Common options:

--logfile LOGFILE
--tmp-dir TMP_DIR
--with-petagene-dir WITH_PETAGENE_DIR
--keep-tmp
--no-seccomp-override
--version

GPU options:

--num-gpus NUM_GPUS