Snakemake workflow: Bioinfo_Macro_Host_Genomics

A Snakemake workflow for Short Variant Discovery in Host Genomes

Usage

• Test that it works:

  • Make sure you have installed snakemake, samtools and bcftools. Either
    • install them with conda/mamba :conda install -c bioconda samtools bcftools).
    • or create an environment (conda create -n 3dohg -c bioconda snakemake samtools bcftools), and activate it (conda activate 3dohg)
  • Generate mock data with bash workflow/scripts/generate_mock_data.sh
  • Run the pipeline: snakemake --use-conda --jobs 8 all. It will download all the necesary software through conda. It should take less than 5 minutes.

• Run it with your own data:

  • Edit config/samples.tsv and add your samples and where are they located.
  • Edit config/features.tsv with information regarding the reference you are using.
  • Run the pipeline: snakemake --use-conda --jobs 8 all.
  • (slurm users): ./run_slurm

Features

• FASTQ processing with fastp
• Mapping with bowtie2
• SAM/BAM/CRAM processing with samtools and picard
• Sample swap detection with gtcheck
• SNP calling with GATK4
• SNP annotation with SNPEff

DAG

References

TBA