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

A pipeline for somatic variantcalling. Category:Single-Sample

An efficient Variant-Caller to highlight low allele-frequency tumor mutations in a clinical practice

Haplotype VCF comparison tools

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.

Somatic variant identification from unpaired samples

SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Computes various SV statistics

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

Annotation and Ranking of Structural Variation

Microsatellite instability (MSI) detection for tumor only data.

VarDict

Detect and visualize microsatellite instability(MSI) from NGS data

Converts 33 offset to 64 and vice versa

Microsatellite Analysis for Normal-Tumor InStability

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

CAVA (Clinical Annotation of VAriants)

HGVS variant name parsing and generation

an empirical Bayesian framework for mutation detection from cancer genome sequencing data

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It u…

Workflow for variant callers MuSE, MuTect, SomaticSniper, and Pindel

A tool to call somatic single nucleotide variants.

A list of deep learning implementations in biology

ONCOCNV - a package to detect copy number changes in Targeted Deep Sequencing and Exome-seq data