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Haplotype LD block without genotypes

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!

gwas haplotype ld
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updated by sathish.periyasamy • sathish.periyasamy • written by alessandrotestori7 alessandrotestori7

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).

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written by Fabio Marroni Fabio Marroni

1 answer

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

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

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written by sathish.periyasamy • sathish.periyasamy

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

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written by alessandrotestori7 alessandrotestori7

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