├── .gitignore ├── ACEseqWorkflow.iml ├── ACEseqWorkflow.jar ├── ACEseqWorkflow_5.0.1.iml ├── CONTRIBUTORS ├── LICENSE.txt ├── README.ACEseqWorkflow.txt ├── Readme.md ├── documentation ├── .DS_Store ├── Makefile ├── make.bat └── source │ ├── .DS_Store │ ├── HRD_LST.rst │ ├── QuickStartGuide.rst │ ├── _static │ └── default.css │ ├── alternativeRunningModes.rst │ ├── conf.py │ ├── finalOutput.rst │ ├── help.rst │ ├── images │ ├── 4108101_MAFplot_balanced.pdf │ ├── 4108101_plot_2.2_0.51_ALL.png │ ├── 4108101_plot_2.2_0.67_ALL.png │ ├── 4108101_plot_4.5_0.34_ALL.png │ ├── 4108101_plot_6.49_0.61_ALL.png │ ├── 4108101_tcn_distances_combined_star.png │ ├── 4112512_gc_corrected.png │ ├── 4112512_plot_1.93_0.9_ALL.png │ ├── 4112512_tcn_distances_combined_star.png │ ├── ACEseq_copyNumberPlot.png │ ├── FWHM_comparison.png │ └── denbi.png │ ├── index.rst │ ├── installation.rst │ ├── license │ ├── license.rst │ ├── methods.rst │ ├── parameters.rst │ ├── purityEvaluation.rst │ ├── qualityCheck.rst │ └── requirements.rst ├── installation ├── ReplicationTime_10cellines_mean_10KB.Rda ├── downloadReferences.sh └── hg19_GRch37_100genomes_gc_content_10kb.txt ├── package_LICENSES.md ├── resources ├── __init__.py ├── analysisTools │ ├── __init__.py │ └── copyNumberEstimationWorkflow │ │ ├── .directory │ │ ├── HRD_estimation.R │ │ ├── PSCBSall.sh │ │ ├── PSCBSgabs_plus_CRESTpoints.py │ │ ├── PSCBSgabs_plus_sv_points.py │ │ ├── PSCBSgaps_SV.sh │ │ ├── __init__.py │ │ ├── addMappability.py │ │ ├── add_haplotypes.py │ │ ├── adjustAlleleFreqs.R │ │ ├── annotateCNA.R │ │ ├── annotate_vcf.pl │ │ ├── artifact.homoDels.potentialArtifacts.txt │ │ ├── centromers.hg19.txt │ │ ├── cluster_functions.R │ │ ├── clusteredPrunedNormal.sh │ │ ├── cnvMergeFilter.sh │ │ ├── cnv_snvMpileup.sh │ │ ├── convertTabToJson.py │ │ ├── correctGCBias.R │ │ ├── correctGCBias_1kb.R │ │ ├── correctGCBias_functions.R │ │ ├── correctGCFlagLimits.Rdata │ │ ├── correct_gc_bias.sh │ │ ├── correct_gc_bias_1kb.sh │ │ ├── createBAFplots.R │ │ ├── createControlBafPlots.sh │ │ ├── createUnphasedFiles.sh │ │ ├── datatablePSCBSgaps.sh │ │ ├── datatable_and_PSCBSgaps.R │ │ ├── embed_haplotypes_vcf.py │ │ ├── environments │ │ ├── conda.sh │ │ ├── conda.yml │ │ ├── conda_tbi-pbs-cluster.sh │ │ └── tbi-cluster.sh │ │ ├── estimateGenotypes.sh │ │ ├── estimateHRDScore.sh │ │ ├── extract_genotype_vcf.py │ │ ├── functions.R │ │ ├── getFinalPurityPloidy.py │ │ ├── getHetSNPs.R │ │ ├── getSex.R │ │ ├── group_genotypes.py │ │ ├── haplotypes.sh │ │ ├── homozygDel.sh │ │ ├── homozygous_deletion.pl │ │ ├── impute2 │ │ ├── impute2.sh │ │ ├── impute2_X.sh │ │ ├── manual_pruning.R │ │ ├── mappy_to_segments.pl │ │ ├── mappy_to_segments.pl.tmp │ │ ├── mergeArtifacts.py │ │ ├── mergePSCBSCrest.sh │ │ ├── merge_and_filter_cnv.py │ │ ├── merge_and_filter_snp.py │ │ ├── parseJson.py │ │ ├── parseVcf.pl │ │ ├── plots.sh │ │ ├── pscbs_all.R │ │ ├── pscbs_plots.R │ │ ├── pscbs_plots_functions.R │ │ ├── purityPloidity.sh │ │ ├── purityPloidity_EstimateFinal.sh │ │ ├── purity_ploidy.R │ │ ├── purity_ploidy_estimation_final.R │ │ ├── python_modules │ │ ├── Options.py │ │ ├── Options.pyc │ │ ├── Tabfile.py │ │ ├── Tabfile.pyc │ │ ├── __init__.py │ │ └── __init__.pyc │ │ ├── removeBreakpoints.py │ │ ├── replaceControl.sh │ │ ├── replaceControlACEseq.R │ │ ├── segmentsDataHomoDel.sh │ │ ├── segmentsPrunedNormal.sh │ │ ├── segments_to_data.py │ │ ├── segments_to_data_homodel.py │ │ ├── smoothData.py │ │ ├── smoothDataMergeSimilar.py │ │ ├── snp_cnv.py │ │ ├── snp_cnv_all.py │ │ ├── snvMergeFilter.sh │ │ └── vcfAnno.sh └── configurationFiles │ └── analysisCopyNumberEstimation.xml └── src └── de └── dkfz └── b080 └── co ├── CopyNumberEstimationWorkflowPlugin.java ├── aceseq ├── ACESeqMethods.groovy ├── ACESeqWorkflow.java └── ACEseqConstants.java └── files ├── BamFile.java ├── BreakpointsFile.java ├── CnvSnpGeneratorResultByType.java ├── CnvSnpGeneratorResultFileGroup.java ├── CoverageWindowsFile.java ├── 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