Question: Haplotype Reconstruction
0
gravatar for mary
6.7 years ago by
mary200
Bologna university
mary200 wrote:

Dear Friends

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

haplotype snp • 2.5k views
ADD COMMENTlink modified 6.7 years ago by Larry_Parnell16k • written 6.7 years ago by mary200

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.

ADD REPLYlink written 6.7 years ago by Larry_Parnell16k

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.

ADD REPLYlink written 6.7 years ago by mary200

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!

ADD REPLYlink written 6.7 years ago by Larry_Parnell16k

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.

ADD REPLYlink written 6.7 years ago by mary200
1
gravatar for Larry_Parnell
6.7 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink written 6.7 years ago by Larry_Parnell16k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1499 users visited in the last hour