Question: Phasing Genotypes With High Recombination Rates (Ld Decays At About 500 Bp Or Less)
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gravatar for hosseinv
6.9 years ago by
hosseinv20
Australia
hosseinv20 wrote:

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

haplotype ld • 2.0k views
ADD COMMENTlink modified 6.9 years ago by Zev.Kronenberg11k • written 6.9 years ago by hosseinv20
1
gravatar for Zev.Kronenberg
6.9 years ago by
United States
Zev.Kronenberg11k wrote:

-- 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

ADD COMMENTlink written 6.9 years ago by Zev.Kronenberg11k

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??

ADD REPLYlink written 6.8 years ago by hosseinv20
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