From 2c4f1c173742af844a65fcb003a71edf0ccbc8da Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Wed, 3 Jun 2015 15:51:24 +0200
Subject: [PATCH] shiva usage of mapping

---
 docs/pipelines/shiva.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/pipelines/shiva.md b/docs/pipelines/shiva.md
index c8ca27b28..25783b879 100644
--- a/docs/pipelines/shiva.md
+++ b/docs/pipelines/shiva.md
@@ -118,6 +118,9 @@ To view all possible config options please navigate to our Gitlab wiki page
 | vcffilter | min_samples_pass | Integer | 1 | Minimum amount of samples which pass custom filter (requires additional flags) |
 | vcffilter | filter_ref_calls | Boolean | true | Remove reference calls |
 
+Since Shiva uses the [Mapping](../mapping.md) pipeline internally, mapping config values can be specified as well.
+For all the options, please see the corresponding documentation for the mapping pipeline.
+
 ### Modes
 
 Shiva furthermore supports three modes. The default and recommended option is `multisample_variantcalling`.
-- 
GitLab