/snakemake-delly

Primary LanguagePython

Structural variation pipeline

This is a snakemake pipeline to process Illumina short-reads and perform SV with Delly

Preparations

  1. Programs are listed in the conda environment in workflow/envs/environment.yaml, it can be used to create a local environment or allow snakemake to create them with --use-conda
  2. Inputs are the Fastq files and a reference genome, all specified in a config.yaml file
  3. Output directory is specified with the -d <dir> parameter for snakemake
  4. The pipeline can be run in a cluster if it is configured

Configuration YAML

samples:
  - sampleID1
  - sampleID2
fastq_dir: /path/to/fastq/dir
genome: ref/genome.fa

Execution

snakemake --configfile <your-config.yaml> -d <output_dir>

Workflow

workflow

Juan Caballero (C) 2024