NVIDIA Clara Parabricks Pipelines: BQSR

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


Quick Start

CLI

$ 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


Options

Option

Description

--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.

--interval-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)

--interval(-L)

Interval within which to call BQSR 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)

--interval-padding(-ip)

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

--out-recal-file (required)

Output BQSR Report File.

--num-gpus

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

--gpu-devices

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.