# Generated by roxygen2: do not edit by hand

export(AnnPhaseVcf)
export(BaseRecal)
export(BedToIntervalList)
export(CalculateContamination)
export(ColSeqArtifact)
export(CombineVariants)
export(DepthOfCoverage)
export(FilterMutectCalls)
export(FilterOBias)
export(Funcotator)
export(GAlign)
export(GPoN)
export(GenomicsDB)
export(GetPileupSummaries)
export(LoFreq)
export(MuSE)
export(Mutect2)
export(Mutect2PL)
export(PoN)
export(RSeQC)
export(ReadBackedPhasing)
export(RenameSampleInVcf)
export(STAR)
export(SamToFastq)
export(SomaticCallers)
export(SomaticSniper)
export(SortVcf)
export(VarDict)
export(VarScan2Somatic)
export(VarScan2_processSomatic)
export(VarScan2_somatic)
export(VarScan2_somaticFilter)
export(alignMerge)
export(annovar)
export(bam_readcount)
export(bcfview)
export(bgzip)
export(blastn)
export(bowtie2)
export(bowtie2_build)
export(bowtie_build)
export(bwa)
export(bwaAlign)
export(bwaMMRecal)
export(bwaMRecal)
export(bwa_index)
export(cnvkit_batch)
export(cutadapt)
export(cwlTools)
export(fastqc)
export(featureCounts)
export(geneBody_coverage)
export(genePredToBed)
export(gtfToGenePred)
export(hapCall)
export(hisat2_align)
export(hisat2_build)
export(htseq)
export(jdCall)
export(kallisto_index)
export(kallisto_quant)
export(lancet)
export(makeblastdb)
export(manta)
export(mantaStrelka)
export(markdup)
export(mergeBam)
export(mergeBamDup)
export(miRDeep2)
export(miRDeep2PL)
export(miRMapper)
export(multiqc)
export(mvOut)
export(neusomatic)
export(phaseVcf)
export(polysolver)
export(pvacseq)
export(read_distribution)
export(rnaseq_Sf)
export(runWDL)
export(salmon_index)
export(salmon_quant)
export(sam2bam)
export(samtools_flagstat)
export(samtools_index)
export(samtools_mpileup)
export(sortBam)
export(starFusion)
export(strelka)
export(tabix_index)
export(vcfCoverage)
export(vcfExpression)
export(vcf_expression_annotator)
export(vcf_readcount_annotator)
export(vep)
export(vt_decompose)
import(BiocFileCache)
import(Rcwl)
import(dplyr)
importFrom(methods,is)
importFrom(rappdirs,user_cache_dir)
importFrom(tximport,tximport)
importFrom(utils,read.table)
importFrom(utils,write.table)
