bqsr performs the Base Quality Score Recalibration (BQSR) in a stand alone fashion.

Quick Start


$ pbrun bqsr --ref Ref/Homo_sapiens_assembly38.fasta \
--in-bam S1.bam \
--knownSites Ref/Homo_sapiens_assembly38.known_indels.vcf.gz \
--out-recal-file recal_gpu.txt \

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 BaseRecalibrator --java-options -Xmx30g --input S1.bam --output \
recal_cpu.txt --known-sites Ref/Homo_sapiens_assembly38.known_indels.vcf.gz \
--reference Ref/Homo_sapiens_assembly38.fasta




--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.

--knownSites (required)

Path to a known indels file. Must be in vcf/vcf.gz format. This option can be used multiple times.

--out-recal-file (required)

Output BQSR Report File.


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