Question: Haplotype LD block without genotypes
0
gravatar for alessandrotestori7
7 months ago by
alessandrotestori7290 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 • 395 views
ADD COMMENTlink modified 6 months ago by sathish.periyasamy20 • written 7 months ago by alessandrotestori7290

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 7 months ago by Fabio Marroni1.8k
2
gravatar for sathish.periyasamy
6 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 6 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 6 months ago by alessandrotestori7290
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