Is it possible to get LD statistics keeping haplotype in mind?
I have SHAPEIT haplotype scaffolds for a 1Mb region. I would like to determine the R2 of pairwises SNPs in a haplotype dependent manner.
Is there an option in PLINK that will produce LD statistics with haplotype in mind?
Or am I missing the point of LD and the results would be the same if the SNPs were not phased?
• 2,314 views
•
link
written
by
QVINTVS_FABIVS_MAXIMVS
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Navigating Haplotype-Based Association Studies: Software Recommendations and Conversion Challenges
written by PKW •
-
Inspect the LD relation between a single pair of SNPs in detail using Plink --ld
written by Tao
-
Estimating LD score in PLINK
written by GabrielMontenegro
-
Get all SNPs that are in high linkage disequilibrium (based on D') for a set of SNPs
written by Mr Locuace
-
Haplotype block in PLINK using r2 values
written by GabrielMontenegro
-
How to determine parent of origin of phased variants when all members are het
written by QVINTVS_FABIVS_MAXIMVS
-
Haplotype Analysis of Phased Genotype Data
written by alakatos •
-
How to determine the haplotypes using Beagle
written by akang
-
How Plink LD-pruning selects which one of the pair SNPs in LD.
written by dadoudou •
-
VCFtools LD calculations only for pairs that include a single SNP of interest
written by Scott
PLINK 1.x is not able to import phase information. LD statistics which take it into account will be a bit different.
Could you try separating the haplotypes into different plink files, then calculate it per (haplotype specific) plink file? You might have to do a lot of slicing and dicing, but you might be able to get it done this way.