Commit 9c0459c7 authored by Sander Bollen's avatar Sander Bollen

adding VEPNormalizer to docs

parent d16ce249
VEPNormalizer
============
Introduction
------------
This tool normalizes a VCF file annotated with the Variant Effect Predictor (VEP).
Since the VEP does not use INFO fields to annotate, but rather puts all its annotations in one big string inside a "CSQ" INFO tag it is necessary to normalize it.
This normalizer will use the information in the CSQ header to create INFO fields for each annotation field.
It has two modes: `standard` and `explode`. The `standard` mode will produce a VCF according to the VCF specification.
This means that every VEP INFO tag will consist of the comma-separated list of values for each transcript.
In case the value is empty, the VEP INFO tag will not be shown for that specific record
Mode `explode` will, on the other hand, create a new VCF record for each transcript it encounters.
This thus means each VEP INFO tag will consist of a single value (if present at all). This can be useful if one must work on a per-transcript basis.
Please note, however, that this means records may seem to be "duplicated".
The CSQ tag is by default removed from the output VCF file. If one wishes to retain it, one can set the `--do-not-remove` option.
Example
---------
~~~~bash
java -jar Biopet-0.3.0.jar tool VEPNormalizer -h
|VEPNormalizer - Parse VEP-annotated VCF to standard VCF format
Usage: VEPNormalizer [options]
-l <value> | --log_level <value>
Log level
-h | --help
Print usage
-v | --version
Print version
-I <vcf> | --InputFile <vcf>
Input VCF file
-O <vcf> | --OutputFile <vcf>
Output VCF file
-m <mode> | --mode <mode>
Mode
--do-not-remove
Do not remove CSQ tag
~~~~
......@@ -19,9 +19,10 @@ pages:
- ['tools/VcfFilter.md','Tools','VcfFilter']
- ['tools/MpileupToVcf.md', 'Tools', 'MpileupToVcf']
- ['tools/sagetools.md', 'Tools', 'Sagetools']
- ['tools/VEPNormalizer.md', 'Tools', 'VEPNormalizer']
- ['tools/WipeReads.md', 'Tools', 'WipeReads']
#- ['developing/Setup.md', 'Developing', 'Setting up your local development environment']
- ['about.md', 'About']
- ['license.md', 'License']
#theme: readthedocs
repo_url: https://git.lumc.nl/biopet/biopet
\ No newline at end of file
repo_url: https://git.lumc.nl/biopet/biopet
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