diff --git a/docs/tools/VepNormalizer.md b/docs/tools/VepNormalizer.md index a7cc5912596a10bfddce6462349013681baa3f9c..e5624e9a5667787073cf36a1441f37bc90514044 100644 --- a/docs/tools/VepNormalizer.md +++ b/docs/tools/VepNormalizer.md @@ -3,11 +3,12 @@ VepNormalizer Introduction ------------ -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 --------- +Help menu: ~~~ bash biopet tool VepNormalizer -h