BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transp

CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.

This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline i

DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classif

Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocation

Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events

Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events

Lancet is a somatic variant caller (SNVs and indels) for short read data

Accurate Variant Calling from Single Cell DNA Sequencing Data. ProSolo: bulk backing vocals for single cell solos. ProSolo is a variant caller for m

A software package with various utilities for processing alignments in the SAM format, including variant calling and alignment viewing.

Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.

VarDict is an ultra sensitive variant caller for both single and paired sample variant calling from BAM files. VarDict implements several novel featur

VarScan, an open source tool for variant detection that is compatible with several short read align-ers.