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.


Defaults to 8.
Number of threads for worker.


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