somatic-variants

Bayesian haplotype-based mutation calling

An ensemble approach to accurately detect somatic mutations using SomaticSeq

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection

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

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

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.

R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)

Snakemake-based workflow for detecting structural variants in genomic data

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

highly-efficient & lightweight mutation signature matrix aggregation

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.

R wrapper for utilizing the SigProfilerMatrixGenerator framework

Transposon Insertion Finder - Detection of new TE insertions in NGS data

Accucopy is a computational method that infers Allele-specific Copy Number alterations from low-coverage low-purity tumor sequencing Data.

Pipeline for Somatic Variant Calling with WES and WGS data

An R wrapper for SigProfilerExtractor that 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 o…

SigProfilerTopography allows evaluating the distribution of somatic mutations and/or mutational signatures across the genomic landscape. The tool evaluates nucleosome occupancy, replication strand bias, transcription strand bias, and replication timing. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.