Yes, you can choose which stocks you sell by giving the proper instructions to your stock broker. The IRS does not prohibit you from choosing the LIFO (last in, first out) method rather than the FIFO method. One disadvantage of the LIFO method is that the lot you are selling is the most recently bought and may be held for less than one year and the capital gains are short-term which are taxed at a higher rate than long term capital gains.
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