Running Parabricks

Parabricks software can be run to use just a single tool or full pipelines. This page will introduce how to run the software to run either option. The first option to pbrun is either the name of the tool or the full pipeline to run.

$ pbrun <tool> <tool-options>
$ pbrun <pipeline> <pipeline-options>

The details of the tools can be found at Tools Overview and the details of the pipelines can be found at Pipeline Overview. Performance optimizations techniques can be found in the Performance Tuning page.

Running a standalone tool

The example below shows how you can run the fq2bam tool.

# Run the fq2bam tool, which aligns, co-ordinate sorts and marks duplicates
# in a pair-ended fastq file. Ref.fa is the bwa-indexed reference file
$ pbrun fq2bam --ref Ref.fa --in-fq sample_1.fq.gz sample_2.fq.gz --out-bam output.bam

Running a pipeline

The example below shows how you can run the germline pipeline.

# Run the germline pipeline for sample_1.fq.gz sample_2.fq.gz to generate
# variant calls using Ref.fa which is the bwa-indexed reference file.
$ pbrun germline --ref Ref.fa --in-fq sample_1.fq.gz sample_2.fq.gz --out-bam output.bam \
--knownSites dbsnp_146.vcf.gz --out-recal-file recal.txt --out-variants result.vcf