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 |
fq2bamfast (BWA-MEM + GATK) | Run newly optimized version of bwa mem, 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 (Beta) | Align long read sequences against a large reference database to convert FASTQ to BAM/CRAM |
mutectcaller | Run GPU-Mutect2 for tumor-normal analysis |
pacbio_germline (Beta) | Run the germline pipeline from FASTQ 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 |