> This page is for version v4.7.1.
> For other versions, use one of these documentation indexes:
> - v4.8.0 (default): https://docs.nvidia.com/clara/parabricks/v4.8.0/llms.txt
> - v4.7.1: https://docs.nvidia.com/clara/parabricks/v4.7.1/llms.txt

> For clean Markdown of any page, append .md to the page URL.
> For a complete documentation index, see https://docs.nvidia.com/clara/parabricks/llms.txt.
> For AI client integration (Claude Code, Cursor, etc.), connect to the MCP server at https://docs.nvidia.com/clara/parabricks/_mcp/server.

# Tool Reference

> **Note**
>
> Many of the default parameter values shown are determined at runtime, based
> on the available number of CPU cores and amount of CPU memory.

## **Tools By Category**

| Category             | Tool                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
| -------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| FASTQ/BAM Processing | \* [applybqsr](/tool-reference/tools/applybqsr) \* [bam2fq](/tool-reference/tools/bam2fq) \* [bamsort](/tool-reference/tools/bamsort) \* [bqsr](/tool-reference/tools/bqsr) \* [fq2bam (BWA-MEM + GATK)](/tool-reference/tools/fq2bam) \* [fq2bam_meth](/tool-reference/tools/fq2bam_meth) \* [giraffe (vg giraffe + GATK)](/tool-reference/tools/giraffe) \* [markdup](/tool-reference/tools/markdup) \* [minimap2](/tool-reference/tools/minimap2)                                                                                                                                                                                                                                                                                                                                                      |
| Variant Calling      | \* [deepsomatic](/tool-reference/tools/deepsomatic) \* [deepvariant](/tool-reference/tools/deepvariant) \* [deepvariant_germline](/tool-reference/tools/deepvariant_germline) \* [germline (GATK Germline Pipeline)](/tool-reference/tools/germline) \* [haplotypecaller](/tool-reference/tools/haplotypecaller) \* [mutectcaller](/tool-reference/tools/mutectcaller) \* [ont_germline](/tool-reference/tools/ont_germline) \* [pacbio_germline](/tool-reference/tools/pacbio_germline) \* [pangenome_aware_deepvariant](/tool-reference/tools/pangenome_aware_deepvariant) \* [pangenome_germline](/tool-reference/tools/pangenome_germline) \* [postpon](/tool-reference/tools/postpon) \* [prepon](/tool-reference/tools/prepon) \* [somatic (Somatic Variant Caller)](/tool-reference/tools/somatic) |
| RNA                  | \* [rna_fq2bam](/tool-reference/tools/rna_fq2bam) \* [starfusion](/tool-reference/tools/starfusion)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| Quality Control      | \* [bammetrics](/tool-reference/tools/bammetrics) \* [collectmultiplemetrics](/tool-reference/tools/collectmultiplemetrics)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
| Variant Processing   | \* [dbsnp](/tool-reference/tools/dbsnp)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
| GVCF Processing      | \* [genotypegvcf](/tool-reference/tools/genotypegvcf) \* [indexgvcf](/tool-reference/tools/indexgvcf)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |

## **Alphabetical List of Tools**

* [applybqsr](/tool-reference/tools/applybqsr)
* [bam2fq](/tool-reference/tools/bam2fq)
* [bammetrics](/tool-reference/tools/bammetrics)
* [bamsort](/tool-reference/tools/bamsort)
* [bqsr](/tool-reference/tools/bqsr)
* [collectmultiplemetrics](/tool-reference/tools/collectmultiplemetrics)
* [dbsnp](/tool-reference/tools/dbsnp)
* [deepsomatic](/tool-reference/tools/deepsomatic)
* [deepvariant](/tool-reference/tools/deepvariant)
* [deepvariant_germline](/tool-reference/tools/deepvariant_germline)
* [fq2bam](/tool-reference/tools/fq2bam)
* [fq2bam_meth](/tool-reference/tools/fq2bam_meth)
* [genotypegvcf](/tool-reference/tools/genotypegvcf)
* [germline](/tool-reference/tools/germline)
* [giraffe](/tool-reference/tools/giraffe)
* [haplotypecaller](/tool-reference/tools/haplotypecaller)
* [indexgvcf](/tool-reference/tools/indexgvcf)
* [markdup](/tool-reference/tools/markdup)
* [minimap2](/tool-reference/tools/minimap2)
* [mutectcaller](/tool-reference/tools/mutectcaller)
* [ont_germline](/tool-reference/tools/ont_germline)
* [pacbio_germline](/tool-reference/tools/pacbio_germline)
* [pangenome_aware_deepvariant](/tool-reference/tools/pangenome_aware_deepvariant)
* [pangenome_germline](/tool-reference/tools/pangenome_germline)
* [postpon](/tool-reference/tools/postpon)
* [prepon](/tool-reference/tools/prepon)
* [rna_fq2bam](/tool-reference/tools/rna_fq2bam)
* [somatic](/tool-reference/tools/somatic)
* [starfusion](/tool-reference/tools/starfusion)