Commit 4ee4ee23 authored by Moustakas's avatar Moustakas
Browse files

Improve phrasing

parent 1d05c0f7
......@@ -3,11 +3,12 @@ VepNormalizer
Introduction
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This tool normalizes a VCF file annotated with the Variant Effect Predictor (VEP).
This tool modifies 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.
Tool will parse the information in the CSQ header to create INFO fields for each annotation field. Tool 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
......@@ -20,6 +21,7 @@ The CSQ tag is by default removed from the output VCF file. If one wishes to ret
Example
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Help menu:
~~~ bash
biopet tool VepNormalizer -h
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