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

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

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

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

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

demo pipeline for testing different data chunking methods for MuTect2

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