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.

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

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

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

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

유전체 데이터 돌연변이 분석

demo pipeline for testing different data chunking methods for MuTect2

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.

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.

Variant calling com Mutect2, PON, BQSR e analise maftools