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biopet.biopet
Commits
a141edb3
Commit
a141edb3
authored
Mar 13, 2015
by
Sander Bollen
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adding toucan to docs
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9c0459c7
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docs/pipelines/toucan.md
docs/pipelines/toucan.md
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mkdocs.yml
mkdocs.yml
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docs/pipelines/toucan.md
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View file @
a141edb3
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>
~~~~
mkdocs.yml
View file @
a141edb3
...
...
@@ -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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