1000G LD constructed using PLINK does not match haploreg
Hi there,
I'm trying to get LD blocks from the 1000G data, and after some searching on the internet I found the genotype data and used PLINK to calculate the LD structure. However, the results do not match haploreg (http://www.broadinstitute.org/mammals/haploreg/haploreg_v3.php), which is, as far as I know, used on the same data.
• 2,069 views
•
link
updated
by
Ram
•
written
by
w.denhollander •
•
written
by
w.denhollander •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to generate haplotypes with SNPs from WGS ?
written by gigotdagneau •
-
Plink 1.9 haplotype blocks with not phased data
written by Peixe
-
How to make association studies using haplotype (LD) blocks instead of SNPs?
written by rimgubaev
-
How to define the LD interval where a SNP locates?
written by Tao
-
Haplotype block in PLINK using r2 values
written by GabrielMontenegro
-
plink calculating LD using R2 command
written by janhuang.cn
-
Population-wise decay of linkage disequilibrium (LD)
written by akang
-
liftover using GWAS summary data and PLINK binary files (bed/bim/fam)
written by Joey
-
How To Calculate All Ld Results For 1000G Raw Genotypes?
written by J.F.Jiang
-
1000 Genomes Ld Calculation
written by Ryan D
It would be easier to answer you if you can give us some more information. To which of the 1000Genomes phases are you referring to? How did you calculate the LD structure? Did you use any filter? Where did you get the output of haploreg? Can you make an example of region where the two maps differ?