Linkage Disequilibrium with Plink

Question

[DOUGLAS]

Good afternoon everyone, I'm new to bioinformatics, I wanted to see if you could help me. I need to do a linkage disequilibrium analysis of some Saccharomyces cerevisae samples I have, I got the data and files (.vcf) using NGSEP (used for QTL mapping) when I was doing other research. Now I need to do this quantification of the LD from this .VCF file containing 4 samples, two haploid, two diploid. I thought about using Plink because I found it in the bibliography, do you guys recommend something to start with plink? tips on the parameters or anything useful that would be nice for me to know? I would also like to know if you know how I can get the Saccharomyces cerevisae SnpId ? as I thought of using the LDSC program. Thank you for your attention.

Answer 1

[chrchang523]

Unfortunately, 4 samples is far too few for LD analysis. (plink2 now prints an error message if you attempt LD analysis with fewer than 50 samples.)

[DOUGLAS]

serious? There are 4 copies of the complete genome of Saccharomyces, wouldn't that be enough in this case?

[chrchang523]

Yes, I'm serious, for the statistical analyses that plink supports.

I have deleted the other misleading answer.