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Recombination Breakpoint Detection

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?

recombination
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updated by Biostar Biostar • written by Lee Katz Lee Katz

2 answers

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

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written by Zev.Kronenberg Zev.Kronenberg

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

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written by Lee Katz Lee Katz

@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.

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written by Genotepes Genotepes

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!

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written by Kartik Sunagar Kartik Sunagar

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