- annotatebamwithumis
- applybqsr
- arriba
- bam2fq
- bammetrics
- bamsort
- bcftoolscall
- bcftoolscsq
- bcftoolsmpileup
- bqsr
- cnnscorevariants
- cnvkit
- collectmultiplemetrics
- consensusreads
- dbsnp
- deeptrio
- deepvariant
- deepvariant_germline
- demuxfastqs
- denovomutation
- duplexconsensusreads
- expansionhunter
- fq2bam
- fq2ubam
- frequencyfiltration
- genotypegvcf
- germline
- glnexus
- groupreadsbyumi
- haplotypecaller
- human_par
- indexgvcf
- kallisto
- lofreq
- lofreq_call
- manta
- muse
- mutectcaller
- postpon
- prepon
- rna_fq2bam
- rna_gatk
- samtoolsmpileup
- setmateinfo
- smoove
- snpswift
- somatic
- somaticsniper
- somaticsniper_workflow
- splitncigar
- starfusion
- strelka
- strelka_workflow
- triocombinegvcf
- umi_fgbio
- variantfiltration
- vcfanno
- vcfqc
- vcfqcbybam
- votebasedvcfmerger
- vqsr
Alphabetical list of all tools
3.8.0