Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

Table 6 Exonerate (v.2.2.0) parameters used for mapping de novo contigs back to the reference genome

Parameter	Value	Parameter	Value
model	affine:local	gappedextension	FALSE
bestn	50; 100 for inversions	joinrangeext	300
gapexend	-3	score	15
dnahspdropoff	10	dna submatrix values (inversions)	5 for match, -15 for mismatch
hspfilter	200

ISSN: 1474-760X