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

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

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 Visual Studio Code via Google Colab.

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.