SimpleSnek

Python
Snakemake
GATK
Variant Calling
Pipeline
Snakemake automated workflow for GATK variant calling pipeline

Snakemake automated workflow for GATK variant calling pipeline

Overview

SimpleSnek is a Snakemake workflow that automates the GATK variant calling pipeline. It provides a reproducible, scalable approach to processing sequencing data from raw reads to called variants.

Key Features

  • Reproducible — Define your workflow once, run it consistently
  • Scalable — Runs on laptops or HPC clusters with minimal changes
  • Parallel — Automatic job scheduling and dependency resolution
  • Resumable — Restart failed runs without re-running completed steps

Pipeline Steps

  1. Quality control — FastQC, trimming
  2. Alignment — BWA-MEM to reference genome
  3. Post-processing — Mark duplicates, BQSR
  4. Variant calling — GATK HaplotypeCaller
  5. Joint genotyping — Combine samples
  6. Filtering — VQSR or hard filtering

Prerequisites

  • Python 3.8+
  • Snakemake
  • GATK 4
  • BWA, samtools

Installation

git clone https://github.com/alex-sandercock/SimpleSnek.git