From bbea216a6c2b7122c0a1bb5d9e58d2040a9c301b Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 3 Jan 2025 13:43:13 -0800
Subject: [PATCH] docs(annotaTR): explain that SNPs aren't supported

---
 trtools/annotaTR/README.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/trtools/annotaTR/README.rst b/trtools/annotaTR/README.rst
index 41a09921..d20ed67e 100644
--- a/trtools/annotaTR/README.rst
+++ b/trtools/annotaTR/README.rst
@@ -39,6 +39,9 @@ Other general parameters:
 
 In addition to specifying input and output options above, you must specify at least one annotation operation to perform. These are described below.
 
+.. note::
+    annotaTR is designed to operate on VCFs composed only of TRs and it will only output TRs. If SNPs are mixed with TRs in the input VCF, you must provide the ``--ref-panel`` option so that annotaTR can subtract out the SNPs and ignore them.
+
 Annotation options
 ------------------