Commit 9733edaf authored by Moustakas's avatar Moustakas
Browse files

Updated the help menu

parent 6e647a07
......@@ -14,26 +14,33 @@ biopet tool VcfToTsv -h
Usage: VcfToTsv [options]
-l <value> | --log_level <value>
Log level
Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'
-h | --help
Print usage
-v | --version
Print version
-I <file> | --inputFile <file>
Input vcf file
-o <file> | --outputFile <file>
output file, default to stdout
-f <value> | --field <value>
-i <value> | --info_field <value>
-f Genotype field name | --field Genotype field name
Genotype field to use
-i Info field name | --info_field Info field name
Info field to use
--all_info
Use all info fields in the vcf header
--all_format
Use all genotype fields in the vcf header
-s <value> | --sample_field <value>
Genotype fields to use in the tsv file
-d | --disable_defaults
Don't output the default columns from the vcf file
--separator <value>
Optional separator. Default is tab-delimited
--list_separator <value>
Optional list separator. By default, lists are separated by a comma
--max_decimals <value>
Number of decimal places for numbers. Default is 2
~~~
To run the tool:
......
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