Tools Overview

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

Tool

Details

fq2bam

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

bqsr

Collect BQSR report on a bam file

applybqsr

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

haplotypecaller

GPU-HaplotypeCaller for calling germline variants

mutectcaller

GPU-Mutect2 for tumor-normal analysis

deepvariant

GPU-DeepVariant for calling germline variants

bammetrics

Collect WGS Metrics on a bam file

collectmultiplemetrics

Collect multiple classes of metrics for a bam file

cnnscorevariants

Filter variants using Convolutional Neural Network

vqsr

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

triocombinegvcf

Combine GVCF of 2 or 3 samples

indexgvcf

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

genotypegvcf

Convert a gvcf to vcf