Welcome to NVIDIA Parabricks v4.3.2
NVIDIA Parabricks v4.3.2

Software Tools

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

The Parabricks somatic (Somatic Variant Caller), germline (GATK Germline Pipeline) and deepvariant_germline tools 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
deepsomatic Run GPU-DeepSomatic for calling somatic variants
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 (BWA-MEM + GATK) Run bwa mem, co-ordinate sorting, marking duplicates, and Base Quality Score Recalibration
fq2bam_meth Run GPU-accelerated bwa-meth compatible alignment, co-ordinate sorting, marking duplicates, and Base Quality Score Recalibration
genotypegvcf Convert a GVCF to VCF
germline (GATK Germline Pipeline) Run the germline pipeline from FASTQ to VCF
haplotypecaller Run GPU-HaplotypeCaller for calling germline variants
indexgvcf Index a GVCF file
markdup Identifies duplicate reads
minimap2 Align long read sequences against a large reference database to convert FASTQ to BAM/CRAM
mutectcaller Run GPU-Mutect2 for tumor-normal analysis
ont_germline (Beta) Run the germline pipeline from FASTQ/BAM to VCF by aligning long read ONT sequences with minimap2 and using a deep neural network analysis
pacbio_germline (Beta) Run the germline pipeline from FASTQ/BAM to VCF by aligning long read sequences with minimap2 and using a deep neural network 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 (Somatic Variant Caller) Run the somatic pipeline from FASTQ to VCF
starfusion Identify candidate fusion transcripts supported by Illumina reads
Previous Software Overview
Next NVIDIA Parabricks WDL/Nextflow Workflows
© Copyright 2024, Nvidia. Last updated on Sep 17, 2024.