Haplotype Reconstruction

Question

[mary]

Dear Friends

I am going to reconstruct haplotype block for linkage disequilibrium analysis , is there any body know. its possible by Plink?

[Larry_Parnell]

I think it would be helpful to tell us some more about your population, how many SNPs you have genotyped (harder to build haplotypes from 100K vs 1 million genotypes, eg), and how many subjects you have.

[mary]

actually I want to do chromosome by chromosome, I have 1000 animal that genotyped and for example in bovine 14 chromosome1500 SNP for this chromosome.

[Larry_Parnell]

Your reply is not so clearly written, but it does seem that there is low SNP density, at least for that chromosome. I don't think that you'll be able to construct and highly confident haplotypes. That said, animals can be inbred and that may help extend the haplotypes. Good luck!

[mary]

I have a population with 1000 animals that was genotyped By bovine 50k. normally I can do phasing by fastPHASE software, but i want to know that plink can do the same analysis. using plink is really simple. for chr. 14 in umd3.1 genome assembly we just have 1519 snp I think,I did it by plink (plink --bfile mydata --blocks), it able to calculate but at final output "plink.blocks" file was empty.

Answer 1

[Larry_Parnell]

In principle, this can be done with Plink. If your population is small, the haplotypes you reconstruct will not be accurate. A large population is necessary. Please also note my comment above.