> 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/tools/llms.txt.
> For AI client integration (Claude Code, Cursor, etc.), connect to the MCP server at https://docs.nvidia.com/clara/parabricks/_mcp/server.

# Tools

## 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):