Pipelines Overview

The following standalone pipelines can be used with the Parabricks software. Please click on the tool names for tool specific options.

Pipeline

Functionality

germline

Detect germline variants for a given sample from fastq files. Compatible with GATK4 best practices.

human_par

Detect germline variants for a given sample from fastq files with correct ploidy values for human sex chromosome handling. Compatible with GATK4 best practices.

somatic

Detect somatic variants for a given tumor/normal fastq files. Compatible with GATK4 best practices.

Population

Studies

Use GenomicsDB to run accelerated Joint Variant Calling.