NVIDIA Clara Parabricks Pipelines: Apply BQSR

applybqsr updates the Base Quality Scores using the BQSR report

Quick Start


$ pbrun applybqsr --ref Ref/Homo_sapiens_assembly38.fasta \
--in-bam S1.bam \
--in-recal-file S1_report.txt \
--out-bam S1_updated.bam \

Compatible GATK4 Command

The command below is the GATK4 counterpart of the Parabricks command above. The output from these commands will generate the exact same results as the output from the above command.

$ gatk ApplyBQSR --java-options -Xmx30g -R Ref/Homo_sapiens_assembly38.fasta \
-I=S1.bam --bqsr-recal-file=S1_report.txt -O=S1_updated.bam




--ref (required)

The reference genome in fasta format. We assume that the indexing required to run bwa has been completed by the user.

--in-bam (required)

Path to the input BAM file.

--in-recal-file (required)

Input BQSR Report File.

--out-bam (required)

Output BAM file.


Path to an interval file for BQSR step with possible 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)


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)


Padding size (in base pairs) to add to each interval you are including (default: None)


Defaults to 8.
Number of threads for worker.


Defaults to number of GPUs in the system.
Number of GPUs to use for a run.


Which GPU devices to use for a run. By default, all GPU devices will be used. To set specific GPU devices, enter a comma-separated list of GPU device numbers.