Software ToolsΒΆ

The following tools are available in the NVIDIA Clara Parabricks software. Click on a tool name for tool-specific options.

In Clara Parabricks somatic, germline and deepvariant_germline are collections of several other individual tools that are commonly used together, all wrapped up as a single tool. For example, the deepvariant_germline takes FASTA and FASTQ files as input and produces a VCF and BAM file as output. Internally, it runs BWA mem alignment, performs coordinate sorting, marks duplicates, and then runs DeepVariant.


Tool

Details

applybqsr

Apply BQSR report to a BAM file and generate a 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

deepvariant_germline

Run the germline pipeline from FASTQ to VCF using a deep neural network analysis

fq2bam

Run bwa mem, co-ordinate sorting, marking duplicates, and Base Quality Score Recalibration

genotypegvcf

Convert a GVCF to VCF

germline

Run the germline pipeline from FASTQ 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 PON file, which is the prerequisite to performing mutect pon

rna_fq2bam

Run RNA-seq data through the fq2bam pipeline

somatic

Run the somatic pipeline from FASTQ to VCF

starfusion

Identify candidate fusion transcripts supported by Illumina reads