Recombination Breakpoint Detection

Question

[Lee Katz]

Hi, I am looking for software to find recombination breakpoints. I found RB-Finder and it looked like the best, but the C code is available only upon request. Has anyone else implemented it in another language? The algorithm is clearly explained, which makes me think that it could have been implemented somewhere else.

Another question: does anyone else have a favorite and available method for detecting recombination breakpoints other than RB-Finder? If so, where is the software and do you have examples of how to run it?

Answer 1

[Zev.Kronenberg]

Have you taken a look at LDHat2.0? I found it pretty robust.

[Lee Katz]

I'm not sure that LDHat finds exact breakpoints. It's just for linkage disequilibrium right? And for quantifying recombination?

[Zev.Kronenberg]

Yup thats right. How about HyPhy for single break point recombination?

http://www.datam0nk3y.org/hyphywiki/index.php/HyPhy#Using_Single_Breakpoint_Recombination_.28SBP.29

[Genotepes]

@Lee. As far as I remember, LDHAT (the McVean's software) is assessing recombination fraction base don LD. I guess this is recombination unsong unerlateds, not in pedigrees.

Answer 2

[Kartik Sunagar]

I suggest trying SBP algorithm implemented in Datamonkey. Its fast and straightforward. There is another algorithm called GARD on the same server, but SBP supersedes GARD. You could also try RDP4 or RAT

All the best!