Commit a141edb3 authored by Sander Bollen's avatar Sander Bollen

adding toucan to docs

parent 9c0459c7
TOUCAN
===========
Introduction
-----------
The Toucan pipeline is a VEP-based annotation pipeline.
Currently, it comprises just two steps:
* Variant Effect Predictor run
* [VEP Normalizer on the VEP output](../tools/VEPNormalizer.md)
Example
-----------
~~~~bash
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
~~~~
Configuration
-------------
You can set all the usual [flags and options](http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html) 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>
~~~~
......@@ -7,6 +7,7 @@ pages:
- ['pipelines/flexiprep.md', 'Pipelines', 'Flexiprep']
- ['pipelines/mapping.md', 'Pipelines', 'Mapping']
- ['pipelines/sage.md', 'Pipelines', 'Sage']
- ['pipelines/toucan.md', 'Pipelines', 'Toucan']
- ['tools/SamplesTsvToJson.md','Tools','SamplesTsvToJson']
- ['tools/BastyGenerateFasta.md','Tools','BastyGenerateFasta']
- ['tools/bedtointerval.md','Tools','BedToInterval']
......
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