DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Copy number variant detection from targeted DNA sequencing

Tools for handling Unique Molecular Identifiers in NGS data sets

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

An ensemble approach to accurately detect somatic mutations using SomaticSeq

HGVS variant name parsing and generation

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection

Tools for processing and analyzing structural variants.

Bayesian genotyper for structural variants

Microsatellite Analysis for Normal-Tumor InStability

Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)

For original Nature Biotechnology Publication (Q1 2012)

BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants

Somatic variant identification from unpaired samples

CAVA (Clinical Annotation of VAriants)

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

Tools for handling Unique Molecular Identifiers in NGS data sets