Entering edit mode
12.0 years ago
mary
▴
210
Dear Friends
I am going to reconstruct haplotype block for linkage disequilibrium analysis , is there any body know. its possible by Plink?
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.
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.
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!
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.