├── .gitattributes ├── .gitignore ├── Dockerfile ├── LICENSE ├── MoCaSeq.sh ├── README.md ├── config.sh ├── data ├── BBDuk-Adapters.fa ├── GRCm38.AgilentProbeGaps.txt ├── GRCm38.Census_allMon_Jan_15_11_46_18_2018_mouse.tsv ├── GRCm38.Genecode_M20_Exons.rds ├── GRCm38.Genecode_M20_Genes.rds ├── GRCm38.Gistic_reference.mat ├── GRCm38.RefFlat ├── GRCm38.SureSelect_Mouse_All_Exon_V1.bed ├── GRCm38.bammatcher_bash.conf ├── GRCm38.bammatcher_docker.conf ├── GRCm38.canonical_chromosomes.bed └── Samples.tsv ├── entrypoint.sh ├── main.nf ├── nextflow.config ├── repository ├── CNV_CleanUp.sh ├── CNV_CopywriterGetModeCorrectionFactor.R ├── CNV_CopywriterGetModeCorrectionFactor.py ├── CNV_CopywriterGetRawData.R ├── CNV_EstimateCoverage.R ├── CNV_GetGenotype.R ├── CNV_GetGenotype.sh ├── CNV_MapSegmentsToGenes.R ├── CNV_PlotCopywriter.R ├── CNV_PlotHMMCopy.R ├── CNV_PlotaCGH.R ├── CNV_RunCopywriter.R ├── CNV_RunHMMCopy.sh ├── Chromothripsis_AnnotateRatios.R ├── Chromothripsis_DetectBreakpointClustering.R ├── Chromothripsis_DetectRandomJoins.R ├── Chromothripsis_FilterDelly.R ├── Chromothripsis_FormatTable.sh ├── Chromothripsis_GetCoverage.sh ├── Chromothripsis_PlotLOHPattern.R ├── Chromothripsis_PlotRearrangementGraph.R ├── Chromothripsis_RearrangementCounter.R ├── Chromothripsis_SimulateCopyNumberStates.R ├── Chromothripsis_WalkDerivativeChromosome.R ├── Cohort_CompareSNPs.r ├── Cohort_CopyResults.sh ├── Cohort_GenerateOverlay.R ├── Cohort_GenerateOverlayLibrary.R ├── Cohort_GetQC.R ├── LOH_CNVKitPrepareLOH.sh ├── LOH_GenerateVariantTable.R ├── LOH_Library.R ├── LOH_MakePlots.R ├── LOH_MapSegmentsToGenes.R ├── Meta_logstats.sh ├── Preparation_DownloadFromENA.sh ├── Preparation_GenerateBWAIndex.sh ├── Preparation_GenerateCopywriterReferences.R ├── Preparation_GenerateSangerMouseDB.sh ├── Preparation_GetExemplaryData.sh ├── Preparation_GetReferenceDataMouse.sh ├── SNV_CleanUp.sh ├── SNV_GenerateCohortDB.sh ├── SNV_GetGenotype.sh ├── SNV_Mutect2Postprocessing.sh ├── SNV_Mutect2PostprocessingSS.sh ├── SNV_RunVEP.sh ├── SNV_SelectOutput.R ├── SNV_SelectOutputSS.R ├── SNV_Signatures.R ├── SNV_StrelkaPostprocessing.sh ├── SV_MantaPostprocessing.sh ├── SV_SelectGenesFromManta.R ├── all_DeterminePhred.sh ├── all_GeneratePlots.R ├── all_MoCaSeq_lcWGS.sh ├── all_RunTitanCNA.R ├── all_RunTitanCNA.sh ├── all_TitanCNA.R └── all_TitanCNASolution.R └── test ├── Mouse.Normal.R1.fastq.gz ├── Mouse.Normal.R2.fastq.gz ├── Mouse.Tumor.R1.fastq.gz └── Mouse.Tumor.R2.fastq.gz /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roland-rad-lab/MoCaSeq/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | 2 | .DS_Store 3 | -------------------------------------------------------------------------------- /Dockerfile: 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