Entering edit mode
5.7 years ago
GabrielMontenegro
▴
670
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.
If the PLINK developer does not respond, you may consider exporting to Haploview and deriving the haploblocks and types there.
--blocks
is the implementation of Haploview!In Haploview, I have derived haploblocks with r2 in the past, though.
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
Indeed, Haploview would crash with too much data...!