jmaassen / sv-callers

A user-friendly, portable and scalable workflow to detect structural variants in whole genome sequencing data

sv-callers

Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases. sv-callers is a Snakemake-based workflow that combines several state-of-the-art tools for detecting SVs in whole genome sequencing (WGS) data. The workflow is easy to use and deploy on any Linux-based machine. In particular, the workflow supports automated software deployment, easy configuration and addition of new analysis tools as well as enables to scale from a single computer to different HPC clusters with minimal effort.

Dependencies

• python (>=3.6)
• conda (>=4.5)
• snakemake (>=4.7)
• xenon-cli (2.4)
• SV callers (installed via the bioconda channel):
  • Manta (1.1.0)
  • DELLY (0.7.7)
  • LUMPY (0.2.13)
  • GRIDSS (1.3.4)

1. Clone this repo.

git clone https://github.com/GooglingTheCancerGenome/sv-callers.git
cd sv-callers/snakemake

2. Install dependencies.

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh # python 3
bash miniconda.sh # install & add conda to your PATH
source ~/.bashrc
conda update -y conda # update conda
conda create -y -n wf && source activate wf # create & activate the environment
conda install -y -c bioconda snakemake
conda install -y -c nlesc xenon-cli # optional but recommended;)

3. Configure and execute the workflow.

• config files: analysis.yaml and environment.yaml
• input files:
  • example data provided in the sv-callers/data directory
  • tumor/normal (T/N) samples in *.bam (incl. index files)
    • list T/N sample pairs to compare in samples.csv
  • reference genome in .fasta (incl. index files)
• output files: somatic SVs in .vcf (incl. index files)

Note: One pair of T/N samples will generate eight SV calling jobs (i.e. 1 x Manta, 1 x LUMPY, 1 x GRIDSS and 5 x DELLY) and one post-processing job that merges DELLY (per SV type) call sets into one VCF file. A workflow instance can be found here.

# dry run doesn't execute anything only checks I/O files
snakemake -np
# dummy run (default) executes 'echo' for each caller and outputs (dummy) *.vcf files
snakemake -C echo_run=1

Submit to Grid Engine-based cluster

#   SV calling:
#     set echo_run=0 and increase the runtime limit e.g. to 60 (in minutes)
#     and/or selectively enable_callers="['manta','delly']" etc.
snakemake -C echo_run=1 --use-conda --latency-wait 30 --jobs  9 \
--cluster 'xenon scheduler gridengine --location local:// submit --name smk.{rule} --inherit-env --option parallel.environment=threaded --option parallel.slots={threads} --max-run-time 1 --max-memory {resources.mem_mb} --working-directory . --stderr stderr-\\\$JOB_ID.log --stdout stdout-\\\$JOB_ID.log' &>smk.log&

Submit to Slurm-based cluster

snakemake -C echo_run=1 --use-conda --latency-wait 30 --jobs  9 \
--cluster 'xenon scheduler slurm --location local:// submit --name smk.{rule} --inherit-env --procs-per-node {threads} --start-single-process --max-run-time 1 --max-memory {resources.mem_mb} --working-directory . --stderr stderr-%j.log --stdout stdout-%j.log' &>smk.log&