Bioinformatics pipelines based on Rcwl


[Up] [Top]

Documentation for package ‘RcwlPipelines’ version 1.3.0

Help Pages

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