variant-calling

GitHub for the SIB courses NGS - Genome variant analysis

Sentieon DNAseq

Sentieon DNAscope + Machine Learning Model

dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCFs) created by DeepVariants are then co_called together using GATK[2]. The resultant trio VCF is then post-processing with FamSeq[3] to eliminate mendelian errors.

Bioinformatics N' Stuff

Whole genome sequencing analysis pipeline for consumer hardware. 100% local, Docker-powered, free and open source.

Some workflows I wrote for my phd projects

Variant calling pipeline for germline enrichment NGS data

Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline

This repository provides an end-to-end workflow for variant calling from single-cell RNA-seq data (scRNA-seq) using Cell Ranger, custom Python BAM splitting, and cellsnp-lite. The pipeline works with 10x Genomics and Drop-seq data and supports human and mouse genomes.

Scripts and containers to run the variant callers originally used in ONCOLINER

Variant calling and PSMC workflows

A CWL implementation of a modular GATK Variant Calling pipeline

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

Variant calling of WGS datasets

GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.

Bash scripts for fastq to vcf pipeline, written for USyd Artemis HPC.

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).

GPU-accelerated germline WGS pipeline for the HG002 reference sample, built with NVIDIA Parabricks

Workflow for biological validation of germline SNP and indel variant datasets.