> For clean Markdown of any page, append .md to the page URL. > For a complete documentation index, see https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/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) ## Docs - [applybqsr](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/applybqsr.md): - [bam2fq](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/bam2fq.md): - [bammetrics](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/bammetrics.md): - [bamsort](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/bamsort.md): - [bqsr](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/bqsr.md): - [collectmultiplemetrics](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/collectmultiplemetrics.md): - [dbsnp](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/dbsnp.md): - [deepsomatic](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/deepsomatic.md): - [deepvariant](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/deepvariant.md): - [deepvariant_germline](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/deepvariant_germline.md): - [fq2bam (BWA-MEM + GATK)](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/fq2bam.md): - [fq2bam_meth](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/fq2bam_meth.md): - [genotypegvcf](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/genotypegvcf.md): - [germline (GATK Germline Pipeline)](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/germline.md): - [giraffe (vg giraffe + GATK)](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/giraffe.md): - [haplotypecaller](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/haplotypecaller.md): - [indexgvcf](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/indexgvcf.md): - [markdup](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/markdup.md): - [minimap2](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/minimap2.md): - [mutectcaller](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/mutectcaller.md): - [ont_germline](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/ont_germline.md): - [pacbio_germline](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/pacbio_germline.md): - [pangenome_aware_deepvariant](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/pangenome_aware_deepvariant.md): - [pangenome_germline](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/pangenome_germline.md): - [postpon](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/postpon.md): - [prepon](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/prepon.md): - [rna_fq2bam](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/rna_fq2bam.md): - [somatic (Somatic Variant Caller)](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/somatic.md): - [starfusion](https://docs.nvidia.com/clara/parabricks/v4.7.1/tool-reference/tools/starfusion.md):