From 423b0006642e012fac179eab3f87b3fa5c9aec99 Mon Sep 17 00:00:00 2001
From: Gleb Kuznetsov <gleb.kuznetsov@gmail.com>
Date: Wed, 5 Jul 2017 13:36:30 -0400
Subject: [PATCH] Update docs with note about SnpEff arguments.

---
 docs/technical_details/snv_calling.rst | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/docs/technical_details/snv_calling.rst b/docs/technical_details/snv_calling.rst
index 204e9cf1..3bbbe512 100644
--- a/docs/technical_details/snv_calling.rst
+++ b/docs/technical_details/snv_calling.rst
@@ -1,3 +1,7 @@
 **************************
 SNV Calling and Annotation
-**************************
\ No newline at end of file
+**************************
+
+SNV calling is performed by Freebayes.
+
+Annotation of variants is performed by SnpEff. The default arguments to SnpEff are specified in the code `here <https://github.com/churchlab/millstone/blob/972cf2e7c38d796ec49aebb77a1aec5742986f13/genome_designer/pipeline/variant_effects.py#L320>`_ and some can be overriden by modifying local_settings.py and restarting the Millstone web server and celery.