NVIDIA Clara Parabricks Pipelines: Software Tools Overview

The following standalone tools can be used with the NVIDIA Clara Parabricks Pipelines software. Please click on the tool names for tool specific options.



Align using bwa-mem, co-ordinate sort and mark duplicates, optionally you can run bqsr.

Collect BQSR report on a bam file

Apply BQSR report on a bam file to generate new bam file

GPU-HaplotypeCaller for calling germline variants

GPU-Mutect2 for tumor-normal analysis

GPU-DeepVariant for calling germline variants

Collect WGS Metrics on a bam file

Collect multiple classes of metrics for a bam file

Filter variants using Convolutional Neural Network

Build a recalibration model to score variant quality and apply a score cutoff to filter variants

Combine GVCF of 2 or 3 samples

Index a vcf/gvcf file


Start a genomic database for multiple samples


Add samples to a genomic database


Select variants from database and create a gvcf

Convert a gvcf to vcf


Mapping RNA reads to a reference, using a two-pass mode to get better alignments around novel splice junctions.


Uses the STAR aligner to identify candidate fusion transcripts.