Question: Haplotype block in PLINK using r2 values
0
gravatar for GabrielMontenegro
12 months ago by
United Kingdom
GabrielMontenegro540 wrote:

I am trying to compute haplotype blocks using PLINK. I found this function very useful --blocks, as it outputs the haplotypes (with the corresponding SNPs within it) in rows and not as a table (as when using --r2). However, it uses D-prime to estimate LD between SNPs.

Is it possible to get haplotype blocks defined by say SNPs with r2 > 0.8 in the same format i.e. haplotypes by rows with the list of SNPs within each haplotype, and not a pair-wise LD table?

Thanks.

ld plink snp haplotypes • 548 views
ADD COMMENTlink written 12 months ago by GabrielMontenegro540

If the PLINK developer does not respond, you may consider exporting to Haploview and deriving the haploblocks and types there.

ADD REPLYlink written 12 months ago by Kevin Blighe52k

--blocks is the implementation of Haploview!

ADD REPLYlink written 12 months ago by GabrielMontenegro540

In Haploview, I have derived haploblocks with r2 in the past, though.

ADD REPLYlink written 12 months ago by Kevin Blighe52k

Oh, I didn't know that thanks. I want to do this genome-wide and I have a large num of SNPs. Not sure if haploview will be able to handle that

ADD REPLYlink written 12 months ago by GabrielMontenegro540

Indeed, Haploview would crash with too much data...!

ADD REPLYlink written 12 months ago by Kevin Blighe52k
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