Open pamelarussell opened 2 years ago
Agreed - I think a multi-pass strategy would work, though I think I would suggest something different:
max-split-read-distance
and read-pair-inner-distance
(or compute the latter)max-split-read-distance
; this parameter should probably be set based on aligner parameters (e.g. a single sequencing error how far from the breakpoint would cause the read to get clipped at that point?)
Currently
AggregateSvPileup
merges breakpoints that have left and right breakpoints within a distance threshold of each other, regardless of the type of read evidence of the breakpoints: split-read (breakpoint occurs inside sequenced read) or read-pair (breakpoint occurs in the unsequenced insert between mates).However, these two types of evidence have different precision of the breakpoint position and should use different distance thresholds. While split-read evidence is likely to point to a very precise position, the position for a read-pair event can be off by as much as the inner distance (insert size minus read lengths). Something similar to the following procedure should be used instead: