Question: Haplotype LD block without genotypes
0
gravatar for alessandrotestori7
10 months ago by
alessandrotestori7300 wrote:

Hi. Is there a tool which can generate haplotype blocks (with plot, like Haploview) without genotype data? I only have a list of SNPs. Thanks!

ld haplotype gwas • 510 views
ADD COMMENTlink modified 9 months ago by sathish.periyasamy20 • written 10 months ago by alessandrotestori7300

Given that LD is the non-random association of alleles at different loci, I would say: NO! However, if you are working in human and you have a list of SNPs, maybe you can browse the 1000 genome data and see if they share haplotype blocks data (I think they do, but I do not know where).

ADD REPLYlink written 10 months ago by Fabio Marroni1.8k
2
gravatar for sathish.periyasamy
9 months ago by
sathish.periyasamy20 wrote:

You could use LDLink's LDMatrix and select the appropriate population

https://analysistools.nci.nih.gov/LDlink/?tab=ldhap

ADD COMMENTlink written 9 months ago by sathish.periyasamy20

Thanks! It works perfectly. However, is it possible to draw a triangular matrix (since it's symmetric) rather than a square matrix?

ADD REPLYlink written 9 months ago by alessandrotestori7300
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: 1659 users visited in the last hour