Software Tools
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.
The following tools are available in the NVIDIA Parabricks software. Click on one of the tool names below for tool-specific options.
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 |
giraffe (vg giraffe + GATK) | Run GPU-accelerated VG-giraffe compatible pangenome alignment and co-ordinate sorting |
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 | 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 | Run the germline pipeline from FASTQ/BAM to VCF by aligning long read sequences with minimap2 and using a deep neural network analysis |
pangenome_aware_deepvariant | Run GPU-Pangenome-aware-deepvariant that uses a pangenome reference for calling germline variants |
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 |