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 |