Software Tools

The following standalone tools can be used with the NVIDIA Clara Parabricks Pipelines software. Click on a tool name for tool-specific options.

Tool	Details
applybqsr	Apply BQSR report to a BAM file and generate 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
fq2bam	Run bwa mem, coordinate sorting, marking duplicates, and Base Quality Score Recalibration
genotypegvcf	Convert a GVCF to VCF
haplotypecaller	Run GPU-HaplotypeCaller for calling germline variants
indexgvcf	Index a GVCF file
mutectcaller	Run GPU-Mutect2 for tumor-normal analysis
postpon	Generate the final VCF output of doing mutect PON
prepon	Build an index for a PON file, which is the prerequisite to performing mutect PON
rna_fq2bam	Run RNA-seq data through the fq2bam pipeline
starfusion	Identify candidate fusion transcripts supported by Illumina reads