Structural variant and indel caller for mapped sequencing data

Strelka2 germline and somatic small variant caller

Structural variation and indel detection by local assembly

Microassembly based somatic variant caller for NGS data

ABRA2

A method for variant graph genotyping based on exact alignment of k-mers

The Platinum Genomes Truthset

ClairS - a deep-learning method for long-read somatic small variant calling

Generic human DNA variant annotation pipeline

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

Dockstore implementation of CGP core WGS analysis

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

A tool to identify and annotate homoplasies on a phylogeny and sequence alignment

A ToolKit to perform a Meta-analysis of Genome-Wide Association Studies

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

Snakemake-based computational workflow for neoantigen prediction from diverse sources

A workflow to analyse sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data

xGAP is an efficient, modular, extensible and fault-tolerant pipeline for massively parallelized genomic analysis/variant discovery from next-generation DNA sequencing data.

🐳 Dockerized WES pipeline for variants identification in mathced tumor-normal samples

Barton and Zeng (2019) - Pipeline for great tit indel analysis.