├── .gitmodules ├── CMakeLists.txt ├── LICENSE ├── Makefile.am ├── README.md ├── benchmark ├── README ├── binarizeSciphiVCF.py ├── binarizeVCF.py ├── compare2GroundTruth.py ├── computePixelDistance.py ├── computeTreeDistance.py ├── computeTreeDistanceGT.py ├── createFalsePNCounts.py ├── createMonovarCluster.r ├── createMonovarCluster_withDen.r ├── createMpileup.py ├── createOverviewGraph.py ├── createOverviewGraph2.py ├── createSCIPhITreeHeatMap.R ├── createSimulationDataSets.snake ├── createSimulationDataSets_100_100.snake ├── createSimulationDataSets_10_10.snake ├── createSimulationDataSets_1_1.snake ├── createSimulationDataSets_2_2.snake ├── createSimulationDataSets_50_50.snake ├── distance.py ├── envs │ └── varscan2.yaml ├── gatherBenchmarkResults.py ├── getMonovarFreqs.py ├── getSciphiFreqs.py ├── monovarToMap.py ├── plotCLBMs.R ├── plotCPNs.R ├── plotDropOuts.R ├── plotDropOutsWithVarScan.R ├── plotNumCells.R ├── plotNumCells_a_b.R ├── plotPriors.R ├── plotTreeDist.R ├── plotVios.R ├── run.sh ├── showNucleotideCounts.py └── tools.py ├── configure.ac ├── real_data ├── SRA053195 │ ├── analysis │ │ ├── README │ │ ├── SRA053195.snake │ │ ├── config.json │ │ ├── run.sh │ │ └── sample_mapping.txt │ └── data │ │ ├── SRA053195.txt │ │ ├── prepare_data.snake │ │ ├── run.sh │ │ └── srr2sample.map ├── SRP044380 │ ├── analysis │ │ ├── README │ │ ├── SRP044380.snake │ │ ├── SRP044380.txt │ │ ├── config.json │ │ ├── panel_regions.bed │ │ ├── panel_to_exclude.vcf │ │ ├── run.sh │ │ └── sample_mapping.txt │ └── data │ │ ├── SRP044380.txt │ │ ├── prepare_data.snake │ │ ├── run.sh │ │ └── srr2sample.map ├── SRP046355 │ ├── analysis │ │ ├── README │ │ ├── SRP046355.snake │ │ ├── compareCellLine.py │ │ ├── config.json │ │ ├── parse.pl │ │ ├── run.sh │ │ └── sample_mapping.txt │ └── data │ │ ├── SRP046355.txt │ │ ├── prepare_data.snake │ │ └── run.sh ├── data │ ├── data.snake │ └── envs │ │ ├── bwa.yaml │ │ └── sra.yaml ├── ovarian_cancer │ ├── config.json │ ├── createMpileup.py │ ├── ovarian.snake │ └── patient9 │ │ ├── getSup.py │ │ ├── pat9.snake │ │ ├── run.sh │ │ └── sample_mapping.txt └── pipe │ ├── align_snake.py │ ├── envs │ ├── bwa.yaml │ ├── gatk.yaml │ ├── multiqc.yaml │ ├── picard.yaml │ ├── qualimap.yaml │ ├── samtools.yaml │ └── sra.yaml │ ├── misc_snake.py │ ├── monovar_snake.py │ ├── prep_data_snake.py │ ├── qc_snake.py │ └── var_exome_snake.py ├── src ├── attachmentScores.h ├── convertTreeIntoClusterMap.cpp ├── createSingleCellSeqTree.cpp ├── findBestTrees.cpp ├── logScores.h ├── mcmc.h ├── noise_counts.h ├── output.h ├── probabilities.h ├── rand.h ├── readData.h ├── sciphi_config.h ├── scoreTree.h ├── trees.h └── version.h └── test └── sciphi_test.cpp /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbg-ethz/SCIPhI/HEAD/.gitmodules -------------------------------------------------------------------------------- /CMakeLists.txt: 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