Bayesian haplotype-based mutation calling

An ensemble approach to accurately detect somatic mutations using SomaticSeq

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

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…

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

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.

SNV calling from single cell sequencing

R data package for pre-compiled somatic mutations from TCGA cohorts and CCLE

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

Snakemake-based workflow for detecting structural variants in genomic data

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.

Dockstore implementation of CGP core WGS analysis

A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

Clinical Whole Genome and Exome Sequencing Pipeline

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.