Software ToolsΒΆ

The following standalone tools can be used with the NVIDIA Clara Parabricks Pipelines software. Click on a tool name for tool-specific options.

Tool

Details

applybqsr

Apply BQSR report to a BAM file and generate new BAM file

bam2fq

Convert a BAM file to FASTQ

bammetrics

Collect WGS Metrics on a BAM file

bamsort

Sort a BAM file

bqsr

Collect BQSR report on a BAM file

collectmultiplemetrics

Collect multiple classes of metrics on a BAM file

dbsnp

Annotate variants based on a dbSNP

deepvariant

Run GPU-DeepVariant for calling germline variants

fq2bam

Run bwa mem, coordinate sorting, marking duplicates, and Base Quality Score Recalibration

genotypegvcf

Convert a GVCF to VCF

haplotypecaller

Run GPU-HaplotypeCaller for calling germline variants

indexgvcf

Index a GVCF file

mutectcaller

Run GPU-Mutect2 for tumor-normal analysis

postpon

Generate the final VCF output of doing mutect PON

prepon

Build an index for a PON file, which is the prerequisite to performing mutect PON

rna_fq2bam

Run RNA-seq data through the fq2bam pipeline

starfusion

Identify candidate fusion transcripts supported by Illumina reads