De novo assembly of a small region after using PINDEL?

[nimrod337]

Hello again,
I have just recently got the program PINDEL to work on my reads, and it identified a large deletion (9kb) in my region of interest (gene family, roughly 40kb). What I would really love, is to take all the reads from PINDEL, and my original alignment from that particular area, and re-align them without the reference, to see if it can make sense of the region. Has anyone had any luck doing such a thing? If so, can you point me in the right direction?
Thanks so much
A

/I've also already designed primers to test if this deletion is legit, so that's obviously a first step.

[m_two]

Try Tigra-SV

http://gmt.genome.wustl.edu/tigra-sv/0.1/index.html

http://genome.cshlp.org/content/24/2/310

[dsenalik]

Tigra looks interesting, but from what I can tell that version is no longer being developed, and the original author now has version 0.3.9 here:

http://bioinformatics.mdanderson.org/main/TIGRA

Also, neither of these will compile with samtools 0.1.19, but 0.1.18 works.
For the benefit of Google searchers, the error message with 0.1.19 is

/usr/lib/samtools/libbam.a(bgzf.o): In function `bgzf_mt':
.../samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
/usr/lib/samtools/libbam.a(bgzf.o): In function `mt_destroy':
.../samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'