Question: Plink 1.9 haplotype blocks with not phased data
gravatar for Peixe
8 months ago by
Peixe600 wrote:


I am trying to calculate haplotype blocks with PLINK 1.9 command --blocks. My data is unphased and I would like to know whether I need my data to be phased in order to correctly estimate blocks this way. I know that the algorithm used is the one from Haploview (Gabriel et al., 2002, Science), and that what PLINK runs is an estimation of the procedure. The Haploview method is based on D' calculations, and to calculate D', with the equation in hand, one would need the haplotype frequencies to compare to the product of allele frequencies.

However, in the Haploview paper of 2004 they explicitly say that

Haploview accepts input in a variety of formats. Pedigree data can be loaded as either partially or fully phased chromosomes or as unphased diplotypes in the standard Linkage format

And also, I came across this paper where PLINK authors explain the procedure in detail:

Briefly, the method involves using 90% confidence intervals for D' (as defined by Wall and Pritchard) to classify pairs of variants as “strong LD”, “strong evidence for historical recombination”, or “inconclusive”; then, contiguous groups of variants where “strong LD” pairs outnumber “recombination” pairs by more than 19 to 1 are greedily selected, starting with the longest base-pair spans.

As far as I understand all this: am I safe in assuming that the --blocks option runs an estimation of the blocks, and thus my data are not strictly required to be phased?


phased ld plink blocks • 268 views
ADD COMMENTlink modified 8 months ago by chrchang5237.6k • written 8 months ago by Peixe600
gravatar for chrchang523
8 months ago by
United States
chrchang5237.6k wrote:

Yes, —blocks is designed for unphased data.

ADD COMMENTlink written 8 months ago by chrchang5237.6k

Great! Thanks Dr. Chang!

ADD REPLYlink written 8 months ago by Peixe600
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