VarSifter and snpEFF v3

[JKTeer]

If you are using VarSifter with snpEFF version 3 or later, you have probably noticed that "Gene_name" is no longer correct. The problem stems from a change in output format in snpEFF version 3. To solve this, you can make a small change in your snpEFF.vs.json file yourself (use a simple text editor.) This file is located in the same place as your VarSifter .jar file.

Change line 38 from

"Gene_name": 5

to

"Gene_name": 6

The next VarSifter release will have a new "snpEFF_v3.vs.json" file that corrects this problem (it makes the above modification.)