An ensemble approach to accurately detect somatic mutations using SomaticSeq

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

Snakemake-based workflow for detecting structural variants in genomic data

ClairS - a deep-learning method for long-read somatic small variant calling

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

Pipeline for Somatic Variant Calling with WES and WGS data

SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of different mutational processes. SigProfilerTopography elucidates the unique topographical characteristics of mutational signatures.

highly-efficient & lightweight mutation signature matrix aggregation

Clinical Whole Genome and Exome Sequencing Pipeline

SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test

accessory scripts for processing varscan somatic/copynumber outputs.

A Platypus-based variant calling pipeline for cancer data

A Platypus-based workflow for indel calling

Galaxy Tool Shed repositories maintained and developed by the Morin Lab.

Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)