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Editing by Base Change or Confidence

Once a location has been found where an edit needs to be made there are two possible methods of resolving the problem. Assuming that the edit is a base replacement, the first way is to simply replace the differing base with the corrected base. This adds the new base at 100% quality. A second solution is to set the confidence of the differing base to 0. Assuming that we have the quality cutoff set to zero or more then this will remove the differing base from the consensus calculation, thus enabling the consensus to be 100% identical.

Both of these methods may be used when replacing bases in the consensus and are selectable using the "Edit Modes" menu. Fixing a problem by adjusting its confidence leaves the original, conflicting, base visible on the screen. However if the changed reading is the only one on a strand then adjusting the confidence means that the point only has good data on one strand.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_67.html