The alignment parameters are similar to the homology filter. To allow a fine tuning of the alignment step, different settings can be used for intra and extrachromosomal junctions, although the default parameters are identical in the two cases. The alignment threshold defines the minimum alignment score (Maximum is 1) to pass the filter. Default is 0.75. The Split minimum value represents the minimum number of nucleotides that must align (either with match or mismatch) to one of the two breakpoint exons to consider the alignment potentially valid. The Split threshold is the fraction of nucleotides that perfectly match to one of the two breakpoint exons. The Split threshold and Split minimum scores are very often different for the two parts of each junction: the filtering is applied to the one with the lowest score.