A disk drive is disclosed comprising a head actuated over a disk. A test pattern is written to the disk and read from the disk to generate a read signal. The read signal is sampled to generate signal samples, the signal samples are filtered with an equalizer filter to generate a first output, and the test pattern is filtered with a target filter to generate a second output. An error signal is generated based on a difference between the first output and the second output. Coefficients of the target filter are adapted in response to the error signal, and after adapting the coefficients of the target filter, a sequence detector is configured based on the coefficients of the target filter.