Snakemake workflow: hg_genotype

A Snakemake workflow for Short Variant Discovery in Host Genomes

Usage

• Test that it works:

  • Make sure you have installed snakemake>=8
  • Run the pipeline: snakemake --use-conda --profile profile/default --jobs 100. 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 --profile profile/default --jobs 8 all.
  • If you are in a cluster with slurm, add --executor slurm.

Features

• FASTQ processing with fastp.
• Mapping with bwa-mem2
• SAM/BAM/CRAM processing with samtools and GATK.
• SNP calling with GATK4.
• SNP annotation with SNPEff and VEP
• Sample swap detection with somalier.
• Reporting with MultiQC.

DAG

References

• fastp
• bwa-mem2
• samtools
• GATK
• SNPEff
• VEP
• somalier
• MultiQC