Q:
I am writing to you because I am working with the BreakSeq software
which was developed by your team and I am having some troubles.

The work-frame of our group is focused on inversions, and recently we have
started using BreakSeq for the annotation of the breakpoint features.
BreakSeq seems to work fine for all its steps except when interfering the
ancestral state of the inversions. I have successfully installed Blat on our
server and also opened the server connection for the three primate genomes.
In addition, I updated the paths of the BreakSeq configuration file which
allows the correct execution of BreakSeq.

However, If I check the ancestral state of some validated inversions from
our database (http://invfestdb.uab.cat), which we known that have different
orientation (standard or inverted) in the primate genomes, BreakSeq
annotates ALL them as Rect "0:0:0". Which I understand that means that the
inversion has the same orientation in all 3 primate genomes.

I will show you an example of what I am trying to explain. If I run breakseq
for the annotation of the inversion HsInv0501
(http://invfestdb.uab.cat/report.php?q=533), which its orientation is
standard for chimpanzee but inverted for orangutan and macaque, I would
expect the following output: Rect "0:1:1". However, BreakSeq output is Rect
"0:0:0".

In conclusion, my main question is the following one: Can BreakSeq predict
the ancestral state in the case of inversions? If it can, where do you think
I am doing something wrong for obtaining every time Rect "0:0:0" as output?

I am attaching the gff input file containing the inversions that are at
least different orientated in one of the three primates, the BreakSeq
configure file which I am using, and also the resulting output folder after
running BreakSeq.

A:
BreakSeq was not intended to look at inversions initially but I suspect it should be usable with some modifications. Alternatively you could reproduce the way Breaseq interprets alignments to primate genomes for interpretation of ancestry