Applying both sliding window and clustering strategies, SVDetect uses anomalously mapped read pairs provided by short read aligners to localize genomic rearrangements and classify their types, for example, large insertions deletions, duplications, and balanced or unbalanced chromosomal translocations.
Applying both sliding-window and clustering strategies, we use anomalously mapped read pairs provided by current short read aligners to localize genomic rearrangements and classify them according to their type, e.g. large insertions deletions, inversions, duplications and balanced or unbalanced inter-chromosomal translocations.
On the other hand, suppose that there is a map such that, for each, the pair provides.
Then if and only if, given different points of, say, there is a map such that, for each : the pair provides.
If is a map homotopic to and is a point such that, we say that the pair provides or that is a pair providing.
Thus, the pair provides (, of course).
For each mapping pair, Perfect mapping read pairs are preferred to Best Match, and both are preferred to Common mapping read pairs.
In addition, large deletions were predicted using a custom Perl script as described previously (Atanur et al., 2010), using mapping flags provided by BWA for paired-end reads (Li and Durbin, 2009).
The prediction performance is illustrated here using the unbiased GIM-SGA data pair, whereas the E-MAP - SGA and E-MAP - GIM pairs are provided in Additional File 6.
