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.
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Tool | Details |
Apply BQSR report to a BAM file and generate a new BAM file | |
Convert a BAM file to FASTQ | |
Collect WGS Metrics on a BAM file | |
Sort a BAM file | |
Collect BQSR report on a BAM file | |
Collect multiple classes of metrics on a BAM file | |
Annotate variants based on a dbsnp | |
Run GPU-DeepVariant for calling germline variants | |
Run the germline pipeline from FASTQ to VCF using a deep neural network analysis | |
Run bwa mem, co-ordinate sorting, marking duplicates, and Base Quality Score Recalibration | |
Convert a GVCF to VCF | |
Run the germline pipeline from FASTQ to VCF | |
Run GPU-HaplotypeCaller for calling germline variants | |
Index a GVCF file | |
Run GPU-Mutect2 for tumor-normal analysis | |
Generate the final VCF output of doing mutect pon | |
Build an index for PON file, which is the prerequisite to performing mutect pon | |
Run RNA-seq data through the fq2bam pipeline | |
Run the somatic pipeline from FASTQ to VCF | |
Identify candidate fusion transcripts supported by Illumina reads |