The Toucan pipeline is a VEP-based annotation pipeline. Currently, it comprises just two steps:


java -jar Biopet-0.3.0.jar pipeline Toucan -h
Arguments for Toucan:
 -Input,--inputvcf <inputvcf>          Input VCF file
 -config,--config_file <config_file>   JSON config file(s)
 -DSC,--disablescatter                 Disable all scatters


You can set all the usual flags and options of the VEP in the configuration, with the same name used by native VEP. As some of these flags might conflict with other Biopet tools/pipelines, it is wise to put the VEP in its own JSON object.

You MUST set the following fields:

  • vep_script: the path to the VEP executable
  • dir or dir_cache: the path to the VEP cache

It is wise to set the cache_version field as well. Furthermore, the fork field will be overwritten by threads in case that one exists in the config. Therefore, it is recommended not to use fork, but to rather use threads.

With that in mind, an example configuration using mode standard of the VepNormalizer would thus be:

    "varianteffectpredictor": {
        "vep_script": <path_to_exe>,
        "dir": <path_to_cache>,
        "cache_version": <cache_version>,
        "threads": 8 
    "vepnormalizer": {
        "mode": "standard"
    "out_dir": <path_to_output_directory>

Running the pipeline

The command to run the pipeline is:

java -jar pipeline Toucan -Input <input_vcf> -config <config_json> -run

If one wishes to run it on a cluster, the command becomes

java -jar pipeline Toucan -Input <input_vcf> -config <config_json> -run -qsub -jobParaEnv <PE>