This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Plink Haplotype block estimation failing to find LD

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.

snp genome software error plink linkage
• 2,999 views • link
updated by chrchang523 chrchang523 • written by lr2767 • lr2767

Hi,

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

• 0 views • link
written by weikai320722 • weikai320722

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

• 0 views • link
written by Shicheng Guo Shicheng Guo

1 answer

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

• 0 views • link
written by chrchang523 chrchang523

Log in to answer this question.

More posts like this