CNV-SNP LD

[Yang Qijie]

Dear sir or madam.
We want to use WGS data to study CNV-SNP LD. How to use PLINK for linkage disequilibrium analysis？

We had generated CNV poupolation vcf and SNP  poupolation vcf. 

What to do next?
I should merge the CNV-SNP vcf to generate merge.vcf and then run plink -vcf merged.vcf --out plink.Ld --r2 --ld-window-r2 0.8 --ld-window-kb 500 --ld-window 999999, right?

[Christopher Chang]

Do you know what you are trying to accomplish with your "linkage disequilibrium analysis"?

[Yang Qijie]

thank you so much！

we want to find sv with tag snp with R2 >0.8.

This really bothers me.

[Christopher Chang]

See plink 1.9's --show-tags command for that.

[Yang Qijie]

1、I tried the-show-tags command of plink 1.9. But I found that there is no r2 value in the output file.  So I tried the command.

first, I use bcftools concat to merge cnv and snp,  and generate  SNP_SV.vcf.

Then,  we use this command "plink -vcf SNP_SV.sort.vcf --out plink.Ld --tag-r2 0.8 --tag-kb 500 --show-tags target.list --list-all --r2 --ld-window-r2 0.8 --ld-window-kb 500 --ld-window 999999", So I could acquire R2 and sv with tag snp. The target.list is the SV_id.

Is this process correct? I look forward to your comments.

2、My understanding is that in fact we are treating the structural variation（start-end） as a point （start） and then doing LD analysis, right? 

thank you ！