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GREEN-VARAN workflow

To perform small variants prioritization as described in the GREEN-DB manuscript, GREEN-VARAN need some annotations to be already present in your input VCF (see "Prioritization of small variants" in main README)

This Nextflow workflow automate the whole process annotating additional information and then performing greenevaran annotation. The workflow is tested on Nextflow >=v20.10

Usage

The typical usage scenario start with a VCF file already containing gene consequences annotations from SnpEff or bcftools. Then from the GREEN-VARAN tool main folder you can perform all annotations using the following command.

This will add a minimum set of information to you VCF including:

  • population allele AF from gnomAD genomes v3.1.1 (GRCh38) or v2.1.1 (GRCh37)
  • functional regions overlaps for TFBS, DNase peaks and UCNE
  • prediction score values for ncER, FATHMM, ReMM
  • GREEN-DB information on regulatory variants with prioritization levels
nextflow workflow/main.nf \
    -profile local \
    --input input_file.vcf.gz \
    --build GRCh38 \
    --out results \
    --scores best \
    --regions best \
    --AF \
    --greenvaran_config config/prioritize_smallvars.json \
    --greenvaran_dbschema config/greendb_schema_v2.5.json

If requested annotation files are missing, they will be automatically downloaded in the default location (resources folder within the main GREEN-VARAN folder)

Note that --input can accept multiple vcf.gz files using a pattern like inputdir/*.vcf.gz

Add additional custom annotations

If you have additional custom annotation you want to add to your VCF before greenvaran processing they can be configured in a .toml and then you can pass this file to the workflow using --anno_toml.

A toml file is a annotation configuration file used by the vcfanno tool and is described in vcfanno repository

A minimal example is reported below

[[annotation]]
file="ExAC.vcf" #source file
fields = ["AF", "AF_nfe"] #INFO fields to be extracted from source
ops=["self", "max"] #How to treat source values
names=["exac_af", "exac_af_nfe_max"] #names used in the annotated file

[[annotation]]
file="regions_score.bed.gz"
columns = [4, 5] #When using a BED or TSV files you can refer to values by col index
names=["regions_ids", "score_max"]
ops=["uniq","max"]

Resources

To perform annotations GREEN-VARAN Nextflow workflow requires a series of supporting files. By default, various resources are expected in the resources folder within the main tool folder. You pass an alternative resource folder using --resource_folder option, bug the same structure is expected in this folder

The expected folder structure is as follows

.. code-block::

.
|-- SQlite
|   `-- GREEN-DB_v2.5.db
|-- GRCh37
|   `-- BED / TSV files used for GRCh37 genome build
`-- GRCh38
    `-- BED / TSV files used for GRCh38 genome build

Use the --list_data option to see the full list of available resources and the expected path for each one.

Automated download

A supporting workflow is provided to automate data download for all resources included in the GREEN-DB collection. You can list the available resources and their resulting download location using

nextflow workflow/download.nf --list_data

The reccomended set of annotations can be downloaded to the default location using the following command or you can set an alternative resource folder using --resource_folder option

nextflow workflow/download.nf \
    -profile local \
    --scores best \
    --regions best \
    --AF \
    --db

Otherwise, single files are available for download from Zenodo repository and all file locations are listed in the GREENDB_collection.txt file under resources folder.

Workflow configuration

The workflow has pre-configured profiles for most popular schedulers (sge, lsf, slurm) and also a local profile (local). These profiles determine how many download jobs can be submitted concurrently and the number of threads used for annotation.

You can activate the desired profile using -profile argument when launching the workflow

NB. You need to update the queue name parameter to reflect your local settings, see how to edit the config below

For more details on how to configure the workflow please refer to the documentation

Available parameters for main workflow

The complete description of availabel parameters can be obtain with --help or in the the documentation