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| RcwlPipelines-package | RcwlPipelines |
| alignMerge | DNASeq alignment, merge and markduplicates |
| annovar | annovar |
| AnnPhaseVcf | AnnPhaseVcf |
| bam_readcount | bam_readcount |
| BaseRecal | Base quality recalibration |
| bcfview | bcftools view |
| BedToIntervalList | Picard BedToIntervalList |
| bgzip | bgzip |
| blastn | blastn |
| bowtie2 | bowtie2 |
| bowtie2_build | bowtie2-build |
| bowtie_build | bowtie-build |
| bwa | bwa mem |
| bwaAlign | bwaAlign |
| bwaMMRecal | DNASeq alignment, merge, markduplicates and recalibration |
| bwaMRecal | DNASeq alignment, markduplicates and recalibration |
| bwa_index | bwa index |
| CalculateContamination | gatk CalculateContamination |
| cnvkit_batch | cnvkit batch |
| ColSeqArtifact | gatk CollectSequencingArtifactMetrics |
| CombineVariants | CombineVariants |
| cutadapt | cutadapt |
| cwlTools | cwlTools |
| DepthOfCoverage | Picard DepthOfCoverage |
| fastqc | fastqc |
| featureCounts | featureCounts |
| FilterMutectCalls | gatk FilterMutectCalls |
| FilterOBias | gatk FilterByOrientationBias |
| Funcotator | gatk Funcotator |
| GAlign | GATK alignment pipeline |
| geneBody_coverage | geneBody_coverage.py |
| genePredToBed | genePredToBed |
| GenomicsDB | gatk GenomicsDBImport |
| GetPileupSummaries | gatk GetPileupSummaries |
| GPoN | GATK4: create a panel of normals |
| gtfToGenePred | gtfToGenePred |
| hapCall | GATK haplotypecaller pipeline |
| hisat2_align | hisat2 |
| hisat2_build | hisat2-build |
| htseq | htseq-count |
| jdCall | GATK joint discovery pipeline |
| kallisto_index | Kallisto index |
| kallisto_quant | Kallisto quant |
| lancet | lancet |
| LoFreq | LoFreq |
| makeblastdb | makeblastdb |
| manta | manta |
| mantaStrelka | strelka somatic caller |
| markdup | picard MarkDuplicates |
| mergeBam | picard MergeSamFiles |
| mergeBamDup | mergeBamDup |
| miRDeep2 | miRDeep2 |
| miRDeep2PL | miRDeep2 |
| miRMapper | miRDeep2 mapper |
| multiqc | multiqc |
| MuSE | MuSE |
| Mutect2 | gatk Mutect2 |
| Mutect2PL | GATK4: Mutect2 |
| mvOut | Rscript: mvOut |
| neusomatic | neusomatic caller |
| phaseVcf | phase VCF |
| polysolver | polysolver |
| PoN | gatk CreateSomaticPanelOfNormals |
| pvacseq | pvacseq |
| RcwlPipelines | RcwlPipelines |
| ReadBackedPhasing | ReadBackedPhasing |
| read_distribution | read_distribution.py |
| RenameSampleInVcf | Picard RenameSampleInVcf |
| rnaseq_Sf | RNASeq pipeline with STAR and featureCounts |
| RSeQC | RNASeq quality control by RSeQC |
| runWDL | java: runWDL |
| salmon_index | salmon index |
| salmon_quant | salmon quant |
| sam2bam | samtools view |
| SamToFastq | picard SamToFastq |
| samtools_flagstat | samtools flagstat |
| samtools_index | samtools index |
| samtools_mpileup | samtools_mpileup |
| SomaticCallers | Combined Somatic Mutation Callers |
| SomaticSniper | SomaticSniper |
| sortBam | samtools sort |
| SortVcf | Picard SortVcf |
| STAR | STAR |
| starFusion | STAR-Fusion |
| strelka | strelka |
| tabix_index | tabix index |
| VarDict | VarDict |
| VarScan2Somatic | VarScan2 somatic caller |
| VarScan2_processSomatic | VarScan2_processSomatic |
| VarScan2_somatic | VarScan2_somatic |
| VarScan2_somaticFilter | VarScan2_somaticFilter |
| vcfCoverage | vcfCoverage |
| vcfExpression | vcfExpression |
| vcf_expression_annotator | vcf_expression_annotator |
| vcf_readcount_annotator | vcf_readcount_annotator |
| vep | vep |
| vt_decompose | vt decompose |