somatic-mutations

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

🌲 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

Microassembly based somatic variant caller for NGS data

DNA sequencing analysis notes from Ming Tang

ClairS: a deep-learning method for long-read tumor–normal pair somatic small variant calling

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

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.

Clone identification from single-cell data

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.

Multi-sample somatic variant caller

Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation

knowledge-based genotyping of cancer hotspots from the tumor BAM files

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

GenomeSpy-based mutation plots for R

A long-read somatic phasing software for tumor-only sequencing

Snakemake workflow for somatic mutation detection without matched normal samples

A long-read somatic phasing software for tumor-normal paired sequencing

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

Tumor-only variant calling