mutect2

Nextflow pipeline for Mutect2 somatic variant calling best practices

secondary analysis pipelines parallelized with apache spark

GATK 4 Mutect2 Somático

This a snakemake pipeline to detect Somatic mutations (GATK4 and Mutect2)

Immunopeptidogenomics pipeline that builds a cryptic peptide database from RNA-seq and identifies non-canonical (cryptic) peptides in immunopeptidomics mass spectrometry data.

A Snakemake pipeline for copy number variant calling without normal tissue samples

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

This repository will house the scripts used to analyze and represent genomic and temperature data for my dissertation.

Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2

cfDNA somatic variant calling (Mutect2 + PoN, CNVkit, Manta, CAPP-Seq filtering, CHIP flagging, tumor fraction) and tumor-microbiome RNA-seq pipelines (Kraken2/Bracken + Kaiju) on SLURM/HPC

Germline variant-calling pipeline (BWA/GATK/bcftools) in Nextflow, with Docker/Singularity profiles — security-reviewed

Variant calling com Mutect2, PON, BQSR e analise maftools

Somatic variant and fusion calling for Illumina cancer panels: DNA (SNVs/indels via GATK) and RNA (gene fusions via STAR + Arriba), with clinical interpretation through PCGR. Panel profiles for 22 kits. Research use only — not a validated diagnostic system.

This repository contains an end-to-end tumour-only somatic variant-calling pipeline (GATK Mutect2 + snpEff) for triple-negative breast cancer whole-exome data, focused on BRCA1/BRCA2/TP53, built on Google Colab via Visual Studio Code.

Research-use full-stack platform for matched tumor–normal somatic variant calling with React, FastAPI, Celery, Nextflow, SLURM, Apptainer, nf-core/sarek, GATK Mutect2, MultiQC, and secure results delivery.

demo pipeline for testing different data chunking methods for MuTect2

유전체 데이터 돌연변이 분석

Reproducible somatic variant calling pipeline using Python, BWA, samtools, minimap2 and GATK Mutect2.

Reproducible Nextflow DSL2 pipeline for short-read human WGS, supporting germline and matched tumor-normal variant calling, benchmarking, SV/CNV analysis, QC, reporting, and provenance.