mutect2

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

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

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

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.

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.

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