Exome/Capture/RNASeq Pipeline Implementation using snakemake

anor: an annotation and visualization system based on R and Shiny framework

Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery

Clinical machine-learning based interpreter of germline mutations.

automatic update Clinvar db for ANNOVAR

Scripts for .bed file genomic region annotation with various tools

End-to-end somatic and germline variant calling pipeline using BWA, GATK HaplotypeCaller, VEP and ANNOVAR for tumor NGS analysis

2018 Genomic Epidemiology Workshop at Academia Sinica

2016 Genomics Epidemiology Workshop

Reference pipeline for somatic SNP detection using BWA for mapping, Mutect2 for calling and Annovar for annotation

Tumor-normal variant analysis workflow using Nextflow DSL2, FastQC, Fastp, BWA, GATK, ANNOVAR and IGV visualization.

Automated variant annotation pipeline, and curated OMIM and ClinVar SNV datasets, developed by Martina Debnath.

tool for converting between dash and non-dash INDEL format using docker

bionano annovar annotation

2017 Genomics Epidemiology Workshop at Academia Sinica

Germline variant calling pipeline using FastQC, BWA, GATK HaplotypeCaller, VEP and ANNOVAR for paired-end NGS data

Reproducible benchmarks: VarNova vs ANNOVAR, VEP, and SnpEff. VarNova is 14× faster than ANNOVAR and 10.7× faster than VEP on full genomic variant annotation pipeline. Includes binary download, benchmark scripts, and test data.