add symbol/hgvs[g] to output

thehyve · Dec 12, 2018 · fed3ac3 · fed3ac3
1 parent 4e4b76c
commit fed3ac3
Showing 1 changed file with 5 additions and 0 deletions.
diff --git 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");