From fed3ac3ad9305fff37d09c171ab2855f81bb4182 Mon Sep 17 00:00:00 2001
From: Ino de Bruijn <ino@ino.pm>
Date: Wed, 12 Dec 2018 17:25:56 -0500
Subject: [PATCH] add symbol/hgvs[g] to output

---
 src/main/java/org/genomenexus/vep_wrapper/VepRunner.java | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/main/java/org/genomenexus/vep_wrapper/VepRunner.java b/src/main/java/org/genomenexus/vep_wrapper/VepRunner.java
index 7779205..9e22b94 100644
--- a/src/main/java/org/genomenexus/vep_wrapper/VepRunner.java
+++ b/src/main/java/org/genomenexus/vep_wrapper/VepRunner.java
@@ -18,6 +18,11 @@ public static String run(List<String> regions, Boolean convertToListJSON) throws
         commands.add("vep");
         commands.add("--cache");
         commands.add("--offline");
+        commands.add("--fasta");
+        commands.add("/opt/vep/.vep/homo_sapiens/92_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz");
+        commands.add("--symbol");
+        commands.add("--hgvs");
+        commands.add("--hgvsg");
         //commands.add("--port");
         //commands.add("3337");
         commands.add("--assembly");