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.
| Category | Tool |
| FASTQ/BAM Processing | |
| Variant Calling | |
| RNA | |
| Quality Control | |
| Variant Processing | |
| GVCF Processing |
- applybqsr
- bam2fq
- bammetrics
- bamsort
- bqsr
- collectmultiplemetrics
- dbsnp
- deepsomatic
- deepvariant
- deepvariant_germline
- fq2bam
- fq2bam_meth
- genotypegvcf
- germline
- giraffe
- haplotypecaller
- indexgvcf
- markdup
- minimap2
- mutectcaller
- ont_germline
- pacbio_germline
- pangenome_aware_deepvariant
- postpon
- prepon
- rna_fq2bam
- somatic
- starfusion