Software Tools
The following tools are available in the Clara 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 |
| 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 (FQ2BAM + BWA-MEM) | Run 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 |
| mutectcaller | Run GPU-Mutect2 for tumor-normal 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 |