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.


Tool

Details

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

creategenomicsdb

Start a genomic database for multiple samples

importgvcftodb

Add samples to a genomic database

selectvariants

Select variants from database and create a gvcf

Convert a gvcf to vcf

STAR

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

STAR-Fusion

Uses the STAR aligner to identify candidate fusion transcripts.