Before building the consensus each read of a pile up should be cropped such that only the part reaching into the gap will be considered. Read sequence outside of this region will be only noise to the pairwise alignment of the reads.
In order to have a "clean" cutting point a trace point of the alignment common to all reads in the pile up should be used. The first/last such trace point should be used for a gap begin/end thus maximizing the common alignment.
Before building the consensus each read of a pile up should be cropped such that only the part reaching into the gap will be considered. Read sequence outside of this region will be only noise to the pairwise alignment of the reads.
In order to have a "clean" cutting point a trace point of the alignment common to all reads in the pile up should be used. The first/last such trace point should be used for a gap begin/end thus maximizing the common alignment.