Welcome Installing Bioconductor Command line tools (Docker) Getting the data

Overview Depth of Sequencing Coverage Cross Sample Contamination Tumor-in-normal Tumor Purity

Overview MuTect Strelka MuTect2

Overview FACETS GATK ACNV

Overview SomaticSignatures (NMF) deconstructSigs (NNLS) SigMa (Likelihood) scarHRD (Homologous Recombination Deficiency) MSIsensor (Microsatellite Instability)

Overview MutSigCV OncodriveFML MutPanning Brown's Method (for combining p-values)

Overview Calculate Mutation Cancer Cell Fractions (CCFs) PhylogicNDT PyClone

Overview GSEA ssGSEA Pathway Overrepresentation

Overview edgeR DESeq2 Independent Hypothesis Weighting (IHW)

Tumor-in-normal

Prerequisites

Prior to running DeTiN to identify tumor-in-normal contamination, we first need to run 3 pipelines:

MuTect: to generate information on somatic mutations called in the tumor, which will be used to rescue mutations incorrectly filtered out due to presence of tumor-in-normal
GATK Somatic CNV (GATK3.8): to generate tangent normalization and segmentation information for the GATK Allelic CNV pipeline
GATK Allelic (GATK4.beta.6): to identify SNP sites and read counts, and generate allelic copy number calls in format readily compatible with DeTiN