Phasing Genotypes With High Recombination Rates (Ld Decays At About 500 Bp Or Less)

Question

[hosseinv]

Dear Biostar folk!

I am now facing an issue with phasing my genotypes. I have a population data (n = 54 individuals) where a vast number of genes were sequenced for. A previous study on same species (which is a tree) shows that recombination rate should be quite high as LD exceeds rarely mare than 500 bp. SNP frequency is quite high as well like 1 in 50 bp as an average.

I was wondering if you could tell me some state-of-the-art packages/softwares dealing with the issue?

Or better to look at IER and SER measurements (after i phased the genes) and skip those genes with unresolved genotypes??

I appreciate your comments on this post and please let me know if I should write more about the data!!

Hossein

Answer 1

[Zev.Kronenberg]

-- recombination estimation --

LDhat

http://ldhat.sourceforge.net

LDhelmet

https://code.google.com/p/ldhelmet/

I like the theme the field has.

-- phasing --

Beagle

http://faculty.washington.edu/browning/beagle/beagle.html

[hosseinv]

Dear Zev.Kronenberg,

Thank you for your suggestions. Looks Beagle is still the method of choice.

Would anybody know how to measure the accuracy of the phased haplotypes??