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Setup resources

ENEO heavily depends on public genetic databases for germline probability estimation plus other fairly common resources daily needed for bioinformatics. In order to make the download and configuration of resources for the workflow as smooth as possible, a python configuration script is available inside setup/download_res.py. As the workflow uses files with different annotations, downloading resources is not enough, as they may need a chromosome naming conversion: thus some common used tools like bcftools are required. To run the automatic setup, first create a conda environment using the setup_env.yml file located inside the setup folder.

conda env create -f setup_env.yml

Then activate the conda environment, and launch the configuration script as follows, replacing the path_for_resources folder with a PATH with at least 60GB of free space and where you have full read/write access.

python3 download_res.py -o <path_for_resources>

Note

The genome assembly in use is the GRCh38. We're not planning to backport it to older assembly.

This script will download different resources:

  • genome from GIAB, the GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18 version. Why? Look here.
  • transcriptome and GTF from Gencode
  • 1000G, ExAC from the GATK resource bundle
  • dbSNPs ALFA from NCBI
  • REDI portal
  • VEP cache (v105)

What if I already got some of them?

The configuration script works by controlling the existence of the files whose path is written inside the main configuration file conf_main.yaml, located in the config folder. If any of those files are already in your machine, just edit the configuration file adding the right absolute path. The script will check for its presence without re-downloading it.

Failure

The annotation for files must be concordant throughout the pipeline, to avoid any error. The chromosome notation in use is the one by Gencode, thus with chr. Be sure to add resources manually only if you're sure of their concordance.