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
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