snpeff

Exome/Capture/RNASeq Pipeline Implementation using snakemake

HgvsGo is a program designed for analyzing "c." and "p." HGVS (Human Genome Variation Society) notations for single nucleotide variations (SNVs) and small insertions/deletions (indels) after variant calling. It serves as an alternative to tools like snpEff and VEP.

Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery

Converts snpeff annotations into MAF

A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.

Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)

A collection of scripts for filtering annotated variant call format files

A tool to import SnpEff annotated files to a Neo4j Graph database

The AlleleCatalog pipeline is built for generating Allele Catalog datasets using next-generation sequencing (NGS) based genetic data and metadata.

Generate an interactive HTML-based report from M.tb SnpEff annotated VCF(s)

R package for mycosnp-nf to parse outputs from snpeffr to desired formats for MDB/Fungi Net

A bioinformatics pipeline for the somatic variant analysis of CD56+ Circulating Tumor Cells (CTCs) in Small Cell Lung Cancer (SCLC) using GATK Mutect2 and SnpEff with AWS S3 & EC2.

Snakemake workflow designed to annotate VCF files withe SnpEff / SniSift

MiModD/SnpEff pipeline for Hawaiian (CB4856) SNP mapping-by-sequencing in C. elegans, identifying causative mutations from a forward-genetic screen (Nonninget et al., Nature Aging, 2025).

A pipeline for filtering annotated variant call format files

X-Men themed variant classifier: sorts a human genome's mutations into mutant tiers using bcftools, SnpEff, and Python

"Clinical Bioinformatics pipeline for identifying CA2 gene mutation in Osteopetrosis using WES data."

End-to-end NGS variant calling and functional annotation pipeline for Limulus polyphemus using GATK and SnpEff, with biological interpretation of high-impact immune and metabolic variants.

NGS-based variant calling pipeline for M. tuberculosis H37Rv - quality control, alignment, variant filtering and functional annotation.

End-to-end WGS NGS variant calling, BQSR, and SnpEff functional annotation pipeline for Salmonella enterica.