The following tools are available in the NVIDIA Parabricks software. Click on a tool name for tool-specific options.
In Parabricks somatic (Somatic Variant Caller), germline (GATK Germline Pipeline) 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 |
Apply BQSR report to a BAM file and generate a new BAM file |
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Convert a BAM file to FASTQ |
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Collect WGS Metrics on a BAM file |
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Sort a BAM file |
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Collect BQSR report on a BAM file |
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Collect multiple classes of metrics on a BAM file |
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Annotate variants based on a dbsnp |
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Run GPU-DeepVariant for calling germline variants |
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Run the germline pipeline from FASTQ to VCF using a deep neural network analysis |
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Run bwa mem, co-ordinate sorting, marking duplicates, and Base Quality Score Recalibration |
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Convert a GVCF to VCF |
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Run the germline pipeline from FASTQ to VCF |
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Run GPU-HaplotypeCaller for calling germline variants |
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Index a GVCF file |
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Run GPU-Mutect2 for tumor-normal analysis |
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Generate the final VCF output of doing mutect pon |
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Build an index for PON file, which is the prerequisite to performing mutect pon |
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Run RNA-seq data through the fq2bam pipeline |
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Run the somatic pipeline from FASTQ to VCF |
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Identify candidate fusion transcripts supported by Illumina reads |