public static void alterObj()
{

try {
    String line;
    LOG.info("Выполняем запрос");
    Process p = Runtime.getRuntime().exec(new String[] {"sqlcmd", "-U", "SA", "-d", "mayadb", "-S", "MSSQLSRV,1433", "-f", "C:/Users/MAYA/workspace/mayaproj/src/main/resources/alterOb.sql"});
       
    BufferedReader input = new BufferedReader (new InputStreamReader(p.getInputStream()));
    while ((line = input.readLine()) != null) {
    System.out.println(line);
    }
    input.close();
  }
  catch (Exception err) {
    err.printStackTrace();
  }
}

Выполняем запрос

new String[] {"sqlcmd", "-U", "SA", "-d", "mayadb", "-S", "MSSQLSRV,1433", "-f", "C:/Users/MAYA/workspace/mayaproj/src/main/resources/alterOb.sql"}

Выполняем запрос