Plink Haplotype block estimation failing to find LD

Question

[lr2767]

Hi all,

I'm trying to estimate the size of the linkage blocks in the genome of a non-model organism. I have SNPs for multiple individuals and I'm running the Plink1.9 function --blocks. The issue is that Plink results says "0 haploblocks written to plink.blocks". I've tried to limit the analysis to the largest scaffolds or a few individuals and I keep getting this error. Am I missing something? Is this even biologically possible? Is it possibly an issue with my data or filtering of SNPs?

plink --allow-extra-chr --blocks no-pheno-req --vcf SNPs_only-3firstscaffolds.vcf

I would appreciate any insight.

[weikai320722]

Hi,

I meet a same problem with you. Have you fix this problem?

[Shicheng Guo]

LD-based computations require at least 50 samples as mentioned by Chris

Answer 1

[chrchang523]

Probably addressed in plink2-users: https://groups.google.com/forum/#!topic/plink2-users/iiU1QBhFagI