The file is being saved twice and should only save once as a .txt in the directory. Thanks.

 '  Create new workbooks based on name
    Dim sSave As String
    Dim sFN As String
    Dim Directory As String
      Beep
      sSave = MsgBox("The data has been formatted and classified. Do you want to save the workbook now?", vbQuestion + vbYesNo)
    If sSave = vbYes Then
              sFN = [CA1] & "hg19annovar.txt"
           Directory = "N:\Torrent\Setup\Clinical\"
ActiveWorkbook.SaveAs Filename:=Directory & sFN, FileFormat:=20
    If sFN = "False" Then Exit Sub
ActiveWorkbook.SaveAs Filename:=Directory & sFN, FileFormat:=20
    Else
        MsgBox "This workbook has not yet been saved!", vbExclamation
    End If