Question: Identification of haplotype blocks
0
gravatar for abascalfederico
20 months ago by
abascalfederico1.0k
Spain
abascalfederico1.0k wrote:

Hi all,

I am working with 1000G data for a chromosomal region. I can see that there are different and (more or less) well defined haplotype blocks within that region. I would like to break the region into these "linked" blocks to do a phylogenetic analysis of each block. Can anyone point to a method to identify those haplotype blocks automatically?

Many, many thanks, Federico

haplotype blocks • 816 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by abascalfederico1.0k
1
gravatar for abascalfederico
20 months ago by
abascalfederico1.0k
Spain
abascalfederico1.0k wrote:

I've found the answer. plink --bfile mydata --blocks

ADD COMMENTlink written 20 months ago by abascalfederico1.0k

Also take a look at haploview (https://www.broadinstitute.org/haploview/haploview). This uses the same algorithm as plink and is good for seeing the LD structure. btw how are you planning to do the phylogenetic analysis?

ADD REPLYlink written 20 months ago by Floris Brenk830
1

Thank you, Floris.

I was planning on using Phyml or RAxML for the phylogenetic analyses, running them for each block separately. However, looking at the alignments I think the blocks are not completely "correct", I mean, there is recombination inside a given block. And recombination mixes phylogenetic histories, so this is a problem.

ADD REPLYlink written 20 months ago by abascalfederico1.0k
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: 1059 users visited in the last hour