From 7e3e31cb5815bb04445fbd091a729f2476a8c278 Mon Sep 17 00:00:00 2001
From: Ioannis Moustakas <i.moustakas@lumc.nl>
Date: Wed, 6 Jul 2016 18:29:26 +0200
Subject: [PATCH] Improved Documentation
---
docs/tools/CheckAllelesVcfInBam.md | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/docs/tools/CheckAllelesVcfInBam.md b/docs/tools/CheckAllelesVcfInBam.md
index 476f8a60c..f3b633d11 100644
--- a/docs/tools/CheckAllelesVcfInBam.md
+++ b/docs/tools/CheckAllelesVcfInBam.md
@@ -1,7 +1,7 @@
# CheckAllelesVcfInBam
## Introduction
-This tool has been written to check the allele frequency in BAM files.
+This tool has been written to check the allele frequency in BAM files. This is meant for comparison with the allele frequency reported at the VCF file
## Example
To get the help menu:
@@ -16,14 +16,15 @@ Usage: CheckAllelesVcfInBam [options]
-v | --version
Print version
-I <file> | --inputFile <file>
-
+ VCF file
-o <file> | --outputFile <file>
-
+ output VCF file name
-s <value> | --sample <value>
-
+ sample name
-b <value> | --bam <value>
-
+ bam file, from which the variants (VCF files) were called
-m <value> | --min_mapping_quality <value>
+ minimum mapping quality score for a read to be taken into account
~~~
To run the tool:
--
GitLab