Software Overview

Parabricks supports the following tools:

The somatic (Somatic Variant Caller), germline (GATK Germline Pipeline), pacbio_germline, ont_germline, and deepvariant_germline tools are a collection of several individual tools that are frequently run together, each grouped as a single command for the users convenience. For example, deepvariant_germline takes FASTA and FASTQ files as input and produces a VCF and BAM file as output. Internally, it runs BWA-MEM alignment, performs coordinate sorting, marks duplicates, and then runs DeepVariant.

Refer to the Tool Reference for lists of all the individual tools. Refer to Parabricks WDL/Nextflow Workflows for information on using Parabricks with WDL and Nextflow. The Output Accuracy and Compatible CPU Software Versions page lists the open-source CPU tools Parabricks is compatible with.