From 9733edafd7bcb37e8616ac49a79b75d921c15d89 Mon Sep 17 00:00:00 2001
From: Ioannis Moustakas <i.moustakas@lumc.nl>
Date: Tue, 19 Jul 2016 16:38:58 +0200
Subject: [PATCH] Updated the help menu
---
docs/tools/VcfToTsv.md | 25 ++++++++++++++++---------
1 file changed, 16 insertions(+), 9 deletions(-)
diff --git a/docs/tools/VcfToTsv.md b/docs/tools/VcfToTsv.md
index a2a367b32..586363fdb 100644
--- a/docs/tools/VcfToTsv.md
+++ b/docs/tools/VcfToTsv.md
@@ -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:
--
GitLab