- applybqsr
- bam2fq
- bammetrics
- bamsort
- bqsr
- collectmultiplemetrics
- dbsnp
- deepsomatic
- deepvariant
- deepvariant_germline
- fq2bam (BWA-MEM + GATK)
- fq2bam_meth
- fq2bamfast (BWA-MEM + GATK)
- genotypegvcf
- germline (GATK Germline Pipeline)
- haplotypecaller
- indexgvcf
- markdup
- minimap2 (Beta)
- mutectcaller
- pacbio_germline (Beta)
- postpon
- prepon
- rna_fq2bam
- somatic (Somatic Variant Caller)
- starfusion
| Category | Tool |
| FASTQ/BAM Processing | |
| Variant Calling | |
| RNA | |
| Quality Control | |
| Variant Processing | |
| GVCF Processing |