Top 20 variant-calling open source projects

De novo genome assembly and multisample variant calling

De novo assembly based variant calling pipeline for Illumina short reads

Sentieon DNAseq

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

Complex structural variant detection from WGS data

dysgu-SV is a collection of tools for calling structural variants using short or long reads

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

find large indels (in the blind spot between GATK/freebayes and SV callers)

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

💾 📃 "Reads to report" for public health and clinical microbiology

Fast and accurate gene fusion detection from RNA-Seq data

PEPPER-Margin-DeepVariant

Population-wide Deletion Calling

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

A tool for fast and accurate summarizing of variant calling format (VCF) files

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

xHLA: Fast and accurate HLA typing from short read sequence data

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products