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

adding VEPNormalizer to docs

parent d16ce249
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.
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>
Do not remove CSQ tag
......@@ -19,9 +19,10 @@ pages:
- ['tools/','Tools','VcfFilter']
- ['tools/', 'Tools', 'MpileupToVcf']
- ['tools/', 'Tools', 'Sagetools']
- ['tools/', 'Tools', 'VEPNormalizer']
- ['tools/', 'Tools', 'WipeReads']
#- ['developing/', 'Developing', 'Setting up your local development environment']
- ['', 'About']
- ['', 'License']
#theme: readthedocs
\ No newline at end of file
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment